TITLE File : mtb53b5_carbo.dat Force field : 53B5 (vacuum simulations) Reference : Oostenbrink et al. J. Comput. Chem. 2004, 25, 1656-1676 File content : molecular topology building blocks (carbohydrates) Format : GROMOS96 Initial file : WFVG, CO, Zuerich, March 2004 Time stamp : PHH, Thu Nov 10 21:55:36 CET 2011 Residue names : according to old GROMOS96 nomenclature (only available in GROMOS96 format) Remark : ***warning*** the 53B5 carbohydrate mtb file deposited in this directory prior to May 2011 was horribly incorrect - this has now been fixed !!! Remark : ***warning*** this file is an auxiliary mtb file - since Nov 2011, these files no longer contain blocks that were redundant with those of the corresponding main mtb file. As a result, make_top must always be called with inclusion of the main mtb file in addition to possible auxiliary ones. Remark : Change from 45A(B)4 involves reparametrization (Lennard-Jones, charges) of the polar amino-acid sidechains, and the renumbering of atom, bond, angle and dihedral types Remark : Parameterization against pure-liquid properties of model compounds Remark : DG, NS, Oct 07: exclusion errors corrected in FMNR, ATP, TMP, THF and HEME Remark : DG, CO, Jan 08: errors in improper dihedrals 21-24 in NADH corrected Remark : The above changes are propagated to subsequent force-field versions Remark : PHH, May 2011 - removed two redundant covalent terms in patches (no effect on GROMOS11 make_top, which removed them anyway) - all isomers & linkages of simple hexopyranoses + some uronates (177 residues, generated by script) - added *many* comments, including extensive information just below the TITLE block Remark : PHH, May 2011 - finalized GROMOS11 file distribution - enforced sequential ordering by (central) atom numbers in covalent terms for all files (no effect on GROMOS11 make_top; make_top enforced it anyway, but now, we avoid the big list of warnings) Modifications : [list below changes after May 2011 - with initials, location and date - and update time stamp] PHH, 27.05.2011: Small correction in header comments (carbohydrate force field information) - data unaltered PHH, 15.09.2011: Correction of the solvent block in G96 and G11 carbo mtb files from 53A5 onward - they still had the IACs appropriate for 45A4 (found by CO) PHH, 09.11.2011: Removed all MTBUILDBLSOLVENT blocks from all auxiliary mtb files (now only included in the main mtb file). As a result, make_top must now always be called with inclusion of the main mtb file (in addition to the possible auxiliary ones). PHH, 09.11.2011: Introduced new residue JA4U for -4-L-iduronate-alpha-1- and uronate trehalo-patches UGB, UKA, UMB, UZA and IJA. END FORCEFIELD 53B5 END TOPPHYSCON # FPEPSI: 1.0/(4.0*PI*EPS0) (EPS0 is the permittivity of vacuum) 0.1389354E+03 # HBAR: Planck's constant HBAR = H/(2* PI) 0.6350780E-01 END LINKEXCLUSIONS #nearest neighbour exclusions when linking #NRNE 2 END # # # Force-field construction: # ========================= # # The parameter set 45A4 is the first one to encompass a # more general description carbohydrates, including residues # for all simple (i.e. unfunctionalized) aldohexopyranoses, # as well as aldohexouronates. # # The calibration and parameters of this set in the # context of carbohydrates are documented in # # Lins, R.D. & Hunenberger, P.H. # A new GROMOS force field for hexopyranose-based carbohydrates. # J. Comput. Chem., 26, 1400-1412 (2005) # # for aldohexopyranoses, and in # # Peric, L., Pereira, C.S., Perez, S. & Hunenberger, P.H. # Conformation, dynamics and ion-binding properties of # single-chain polyuronates: a molecular dynamics study # Mol. Simul., 34, 421-446 (2008) # # for aldohexouronates. # # This set adheres to well-defined build-up rules. # Three peculiarities to be noted are: # # (i) the torsional potential energy terms controling the orientation # of the hydroxymethyl dihedral angle omega in aldohexopyranoses are # different for anti-C4,C5 (e.g. Glc) and syn-C4,C5 (e.g. Gal) residues; # (ii) the torsional potential energy terms controling the orientation # of the glycosidic dihedral angle phi are different # for alpha and beta anomers; # (iii) a special third-neighbor exclusion is introduced # between the lactol hydrogen and ring oxygen atoms # of a reducing residue. # # The 53A5, 53A6 and 54A7 versions of the force field # are nearly identical to 45A4 in the context of # carbohydrates. # # The only change affecting these compounds is the # alteration of the Lennard-Jones C12 interaction parameter # of atom-type OA (all oxygen atoms in sugars) with non-polar # atoms (e.g. aliphatic carbon united atoms), beyond third # neighbors only. This change is expected to have a limited # impact on the simulation results. # # The B-version of the force field are also available for (approximate) # simulations in vacuum. The only change between A- and B-versions # is a a neutralization of the carboxylate charge in uronate # residues. # # Naming convention for carbohydrate residues : # ============================================= # # First letter (stereochemistry): # # A: D-allose B: L-allose # R: D-altrose S: L-altrose # G: D-glucose H: L-glucose # M: D-mannose N: L-mannose # Y: D-gulose Z: L-gulose # I: D-idose J: L-idose # K: D-galactose L: L-galactose # T: D-talose U: L-talose # # Second letter (anomery): # A: alpha # B: beta # # Third letter (connectivity): # 2: at 2-OH # 3: at 3-OH # 4: at 4-OH # 6: at 6-OH # # Fourth letter (functionalization): # \ plain hexopyranose # U uronate # # -> only the four most relevant residues, # GB4U, KA4U, MB4U, ZA4U (glucuronates, alginates, pectinates) and JA4U (dermatan sulfate) # are available at present for the uronates # # In the following, we use the generic notations: # @ : stereochemistry [A,R,G,M,Y,I,K,T,B,S,H,N,Z,J,L,U] # * : anomery [A,B] # # : connectivity [1,2,3,4,6] # # Patches: # # C#OH : initial HO#-O#-C#- group (# not equal to 1; for patching a # residue of type @*#) # C1OH : terminal -C1-O1-HO1 (HO1=hydrogen) # C1OC : terminal -C1-O1-CM (CM=methyl) # C@* : terminal -C1-O1-C1'-... (trehalo 1->1' linkage with additional # terminal residue of type @*) # # Residue and patch construction: # =============================== # # The residues are assembled in the direction # # non-reducing end -> reducing end # # (for a chain terminated by a trehalo linkage, # leading to a formally non-reducing oligosaccharide, # the trehalo linkage is also at the chain end) # # The (linear) sequence is defined as # # initial patch - [residues] - terminal patch # # For each residue @*#: # (prev -> previous residue or initial patch; # next -> next residue or terminal patch) # # - the C1_prev-O# and O#-C# bonds are *not* defined in the residue (but in the prev) # - the C1_prev-O#-C# angle is *not* defined in the residue (but in the prev) # - the O5_prev-C1_prev-O#-C# dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # - the C1_prev-O#-C#-C# dihedral (prev glycosidic psi dihedral) *is* defined in the residue # - the exclusions of C1_prev and O# *are* defined in the residue # # and # # - the C1_O1 and O1-C#_next bonds *are* defined in the residue # - the C1-O1-C#_next angle *is* defined in the residue # - the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # - the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # - the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # # For each initial patches C#OH: # # - the HO#-O# and O#-C# bonds *are* defined in the patch # - the HO#-O#-C# angle *is* defined in the patch # - the HO#-O#-C#-C(#-1) (chi# dihedral) is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the exclusions of HO# and O# *are* defined in the patch (replace those defined in the residue, which are identical) # - the exclusions of C# are *not* defined in the patch (but in the residue) # # For the terminal patch C1OH: # # - the O1-H1 bond *is* defined in the patch as a replacement # - the C1-O1-H1 angle *is* defined in the patch as a replacement # - the O5-C1-O1-H1 dihedral (phi dihedral) is *not* defined in the patch (but in the residue) # - the exclusions of O5, C1, O1 and HO1 *are* defined in the patch (replace those defined in the residue, # which are identical up to one exception: a special 1-4 exclusion (ring oxygen O5 to lactol hydrogen HO1 # specific to this force-field is introduced) # # For the terminal patch C1OC: # # - the O1-CM bond is *not* defined in the patch (but in the residue) # - the C1-O1-CM angle is *not* defined in the patch (but in the residue) # - the O5-C1-O1-CM dihedral (phi dihedral) is *not* defined in the patch (but in the residue) # - the exclusions of C1, O1 and CM *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # For the terminal patches C@*: # # - the O1-CM bond is *not* defined in the patch (but in the residue) # - the C1-O1-CM angle is *not* defined in the patch (but in the residue) # - the O5-C1-O1-CM dihedral (phi dihedral) is *not* defined in the patch (but in the residue) # - the exclusions of C1, O1 and CM *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # Residue and patch assembly: # =========================== # # The residues are assembled in the direction # # non-reducing end -> reducing end # # (for a chain terminated by a trehalo linkage, # leading to a formally non-reducing oligosaccharide, # the trehalo linkage is also at the chain end) # # The (linear) sequence is defined as # # initial patch - [residues] - terminal patch # # Examples: # # beta-D-glucopyranose: C4OH GB4 C1OH # alpha-D-glucopyranose: C4OH GA4 C1OH # Me-beta-D-glucopyranoside: C4OH GB4 C1OC # Me-alpha-D-glucopyranoside: C4OH GA4 C1OC # beta-cellobiose: C4OH GB4 GB4P C1OH # beta-maltose: C4OH GA4 GB4P C1OH # trehalose (alpha,alpha): C4OH GA4 CGA # isotrehalose (alpha,beta): C4OH GA4 CGB [or C4OH GB4 CGAP] # neotrehalose (beta,beta): C4OH GB4 CGB # # Note that the first residue can be terminated in different # ways. For example, C2OH GB2 GB4 C1OH is also beta-cellobiose # (although the atom numbering will be different) # # Next force-field version: # ========================= # # The next force field version is 56A6@CARBO, as documented in # # Hansen, H.S. & Hunenberger, P.H. # A reoptimized GROMOS force field for hexopyranose-based carbohydrates # accounting for the relative free energies of ring conformers, anomers, # epimers, hydroxymethyl rotamers and glycosidic linkage conformers. # J. Comput. Chem., 32, 998-1032 (2011) # # The corresponding force-field files will soon be available. # MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME AA2 # -2-D-allopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 1 2 # C2-O2-C3-C1 1 0 5 13 2 # C3-C2-O3-C4 5 1 6 2 2 # C5-O4-C3-C4 11 3 5 2 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME AA3 # -3-D-allopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 1 6 5 2 # C4-O3-C2-C3 2 0 5 1 2 # C4-C3-O4-C5 2 1 3 11 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME AA4 # -4-D-allopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 2 6 5 2 # C4-O3-C2-C3 1 3 5 2 2 # C5-O4-C3-C4 11 0 2 1 2 # C4-C6-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME AA6 # -6-D-allopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 2 6 5 2 # C4-O3-C2-C3 8 3 5 2 2 # C4-C3-O4-C5 8 2 9 11 2 # C4-C6-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 0 1 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 0 1 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CAA # # terminal -C1-O1-C1'(AA) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type AA # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C4'-O3'-C2'-C3' 8 12 14 11 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME AB2 # -2-D-allopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 1 12 14 13 2 # C2-O2-C3-C1 1 0 5 13 2 # C3-C2-O3-C4 5 1 6 2 2 # C5-O4-C3-C4 11 3 5 2 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME AB3 # -3-D-allopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 1 6 5 2 # C4-O3-C2-C3 2 0 5 1 2 # C4-C3-O4-C5 2 1 3 11 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME AB4 # -4-D-allopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 2 6 5 2 # C4-O3-C2-C3 1 3 5 2 2 # C5-O4-C3-C4 11 0 2 1 2 # C4-C6-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME AB6 # -6-D-allopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 2 6 5 2 # C4-O3-C2-C3 8 3 5 2 2 # C4-C3-O4-C5 8 2 9 11 2 # C4-C6-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 0 1 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 0 1 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CAB # # terminal -C1-O1-C1'(AB) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type AB # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1'-O1-O5'-C2' 5 4 6 14 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C4'-O3'-C2'-C3' 8 12 14 11 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 2 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 32 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME RA2 # -2-D-altropyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 1 2 # C1-O2-C3-C2 13 0 5 1 2 # C3-C2-O3-C4 5 1 6 2 2 # C5-O4-C3-C4 11 3 5 2 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME RA3 # -3-D-altropyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 1 6 13 2 # C4-O3-C2-C3 2 0 5 1 2 # C4-C3-O4-C5 2 1 3 11 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME RA4 # -4-D-altropyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 2 6 13 2 # C4-O3-C2-C3 1 3 5 2 2 # C5-O4-C3-C4 11 0 2 1 2 # C4-C6-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME RA6 # -6-D-altropyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 2 6 13 2 # C4-O3-C2-C3 8 3 5 2 2 # C4-C3-O4-C5 8 2 9 11 2 # C4-C6-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 0 1 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 0 1 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CRA # # terminal -C1-O1-C1'(RA) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type RA # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C2'-C3'-O2'-C1' 14 11 15 5 2 # C4'-O3'-C2'-C3' 8 12 14 11 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME RB2 # -2-D-altropyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 1 12 14 13 2 # C1-O2-C3-C2 13 0 5 1 2 # C3-C2-O3-C4 5 1 6 2 2 # C5-O4-C3-C4 11 3 5 2 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME RB3 # -3-D-altropyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 1 6 13 2 # C4-O3-C2-C3 2 0 5 1 2 # C4-C3-O4-C5 2 1 3 11 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME RB4 # -4-D-altropyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 2 6 13 2 # C4-O3-C2-C3 1 3 5 2 2 # C5-O4-C3-C4 11 0 2 1 2 # C4-C6-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME RB6 # -6-D-altropyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 2 6 13 2 # C4-O3-C2-C3 8 3 5 2 2 # C4-C3-O4-C5 8 2 9 11 2 # C4-C6-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 0 1 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 0 1 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CRB # # terminal -C1-O1-C1'(RB) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type RB # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1'-O1-O5'-C2' 5 4 6 14 2 # C2'-C3'-O2'-C1' 14 11 15 5 2 # C4'-O3'-C2'-C3' 8 12 14 11 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 2 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 32 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME GA2 # -2-D-glucopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 1 2 # C2-O2-C3-C1 1 0 5 13 2 # C4-C2-O3-C3 2 1 6 5 2 # C5-O4-C3-C4 11 3 5 2 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME GA3 # -3-D-glucopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 1 6 5 2 # C3-O3-C2-C4 1 0 5 2 2 # C4-C3-O4-C5 2 1 3 11 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME GA4 # -4-D-glucopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 1 2 # C5-O4-C3-C4 11 0 2 1 2 # C4-C6-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME GA6 # -6-D-glucopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 8 2 # C4-C3-O4-C5 8 2 9 11 2 # C4-C6-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 0 1 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 0 1 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CGA # # terminal -C1-O1-C1'(GA) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type GA # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME GB2 # -2-D-glucopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 1 12 14 13 2 # C2-O2-C3-C1 1 0 5 13 2 # C4-C2-O3-C3 2 1 6 5 2 # C5-O4-C3-C4 11 3 5 2 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME GB3 # -3-D-glucopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 1 6 5 2 # C3-O3-C2-C4 1 0 5 2 2 # C4-C3-O4-C5 2 1 3 11 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME GB4 # -4-D-glucopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 1 2 # C5-O4-C3-C4 11 0 2 1 2 # C4-C6-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME GB6 # -6-D-glucopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 8 2 # C4-C3-O4-C5 8 2 9 11 2 # C4-C6-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 0 1 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 0 1 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CGB # # terminal -C1-O1-C1'(GB) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type GB # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1'-O1-O5'-C2' 5 4 6 14 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 2 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 32 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME MA2 # -2-D-mannopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 1 2 # C1-O2-C3-C2 13 0 5 1 2 # C4-C2-O3-C3 2 1 6 5 2 # C5-O4-C3-C4 11 3 5 2 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME MA3 # -3-D-mannopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 1 6 13 2 # C3-O3-C2-C4 1 0 5 2 2 # C4-C3-O4-C5 2 1 3 11 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME MA4 # -4-D-mannopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 2 6 13 2 # C3-O3-C2-C4 2 3 5 1 2 # C5-O4-C3-C4 11 0 2 1 2 # C4-C6-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME MA6 # -6-D-mannopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 2 6 13 2 # C3-O3-C2-C4 2 3 5 8 2 # C4-C3-O4-C5 8 2 9 11 2 # C4-C6-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 0 1 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 0 1 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CMA # # terminal -C1-O1-C1'(MA) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type MA # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C2'-C3'-O2'-C1' 14 11 15 5 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME MB2 # -2-D-mannopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 1 12 14 13 2 # C1-O2-C3-C2 13 0 5 1 2 # C4-C2-O3-C3 2 1 6 5 2 # C5-O4-C3-C4 11 3 5 2 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME MB3 # -3-D-mannopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 1 6 13 2 # C3-O3-C2-C4 1 0 5 2 2 # C4-C3-O4-C5 2 1 3 11 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME MB4 # -4-D-mannopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 2 6 13 2 # C3-O3-C2-C4 2 3 5 1 2 # C5-O4-C3-C4 11 0 2 1 2 # C4-C6-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME MB6 # -6-D-mannopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 2 6 13 2 # C3-O3-C2-C4 2 3 5 8 2 # C4-C3-O4-C5 8 2 9 11 2 # C4-C6-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 0 1 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 0 1 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CMB # # terminal -C1-O1-C1'(MB) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type MB # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1'-O1-O5'-C2' 5 4 6 14 2 # C2'-C3'-O2'-C1' 14 11 15 5 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 2 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 32 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME YA2 # -2-D-gulopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 1 2 # C2-O2-C3-C1 1 0 5 13 2 # C3-C2-O3-C4 5 1 6 2 2 # C4-O4-C3-C5 2 3 5 11 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME YA3 # -3-D-gulopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 1 6 5 2 # C4-O3-C2-C3 2 0 5 1 2 # C5-C3-O4-C4 11 1 3 2 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME YA4 # -4-D-gulopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 2 6 5 2 # C4-O3-C2-C3 1 3 5 2 2 # C4-O4-C3-C5 1 0 2 11 2 # C4-C6-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 1 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME YA6 # -6-D-gulopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 2 6 5 2 # C4-O3-C2-C3 8 3 5 2 2 # C5-C3-O4-C4 11 2 9 8 2 # C4-C6-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 0 1 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 0 1 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 0 1 11 8 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CYA # # terminal -C1-O1-C1'(YA) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type YA # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C4'-O3'-C2'-C3' 8 12 14 11 2 # C4'-O4'-C3'-C5' 8 9 11 7 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 3 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 35 # # terms of type : C4'-C5'-C6'-O6' (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # C4'-C5'-C6'-O6' 8 7 17 18 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME YB2 # -2-D-gulopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 1 12 14 13 2 # C2-O2-C3-C1 1 0 5 13 2 # C3-C2-O3-C4 5 1 6 2 2 # C4-O4-C3-C5 2 3 5 11 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME YB3 # -3-D-gulopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 1 6 5 2 # C4-O3-C2-C3 2 0 5 1 2 # C5-C3-O4-C4 11 1 3 2 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME YB4 # -4-D-gulopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 2 6 5 2 # C4-O3-C2-C3 1 3 5 2 2 # C4-O4-C3-C5 1 0 2 11 2 # C4-C6-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 1 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME YB6 # -6-D-gulopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 2 6 5 2 # C4-O3-C2-C3 8 3 5 2 2 # C5-C3-O4-C4 11 2 9 8 2 # C4-C6-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 0 1 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 0 1 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 0 1 11 8 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CYB # # terminal -C1-O1-C1'(YB) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type YB # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1'-O1-O5'-C2' 5 4 6 14 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C4'-O3'-C2'-C3' 8 12 14 11 2 # C4'-O4'-C3'-C5' 8 9 11 7 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 3 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 35 # # terms of type : C4'-C5'-C6'-O6' (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # C4'-C5'-C6'-O6' 8 7 17 18 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 2 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 32 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME IA2 # -2-D-idopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 1 2 # C1-O2-C3-C2 13 0 5 1 2 # C3-C2-O3-C4 5 1 6 2 2 # C4-O4-C3-C5 2 3 5 11 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME IA3 # -3-D-idopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 1 6 13 2 # C4-O3-C2-C3 2 0 5 1 2 # C5-C3-O4-C4 11 1 3 2 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME IA4 # -4-D-idopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 2 6 13 2 # C4-O3-C2-C3 1 3 5 2 2 # C4-O4-C3-C5 1 0 2 11 2 # C4-C6-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 1 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME IA6 # -6-D-idopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 2 6 13 2 # C4-O3-C2-C3 8 3 5 2 2 # C5-C3-O4-C4 11 2 9 8 2 # C4-C6-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 0 1 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 0 1 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 0 1 11 8 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CIA # # terminal -C1-O1-C1'(IA) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type IA # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C2'-C3'-O2'-C1' 14 11 15 5 2 # C4'-O3'-C2'-C3' 8 12 14 11 2 # C4'-O4'-C3'-C5' 8 9 11 7 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 3 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 35 # # terms of type : C4'-C5'-C6'-O6' (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # C4'-C5'-C6'-O6' 8 7 17 18 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME IB2 # -2-D-idopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 1 12 14 13 2 # C1-O2-C3-C2 13 0 5 1 2 # C3-C2-O3-C4 5 1 6 2 2 # C4-O4-C3-C5 2 3 5 11 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME IB3 # -3-D-idopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 1 6 13 2 # C4-O3-C2-C3 2 0 5 1 2 # C5-C3-O4-C4 11 1 3 2 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME IB4 # -4-D-idopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 2 6 13 2 # C4-O3-C2-C3 1 3 5 2 2 # C4-O4-C3-C5 1 0 2 11 2 # C4-C6-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 1 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME IB6 # -6-D-idopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 2 6 13 2 # C4-O3-C2-C3 8 3 5 2 2 # C5-C3-O4-C4 11 2 9 8 2 # C4-C6-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 0 1 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 0 1 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 0 1 11 8 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CIB # # terminal -C1-O1-C1'(IB) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type IB # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1'-O1-O5'-C2' 5 4 6 14 2 # C2'-C3'-O2'-C1' 14 11 15 5 2 # C4'-O3'-C2'-C3' 8 12 14 11 2 # C4'-O4'-C3'-C5' 8 9 11 7 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 3 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 35 # # terms of type : C4'-C5'-C6'-O6' (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # C4'-C5'-C6'-O6' 8 7 17 18 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 2 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 32 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME KA2 # -2-D-galactopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 1 2 # C2-O2-C3-C1 1 0 5 13 2 # C4-C2-O3-C3 2 1 6 5 2 # C4-O4-C3-C5 2 3 5 11 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME KA3 # -3-D-galactopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 1 6 5 2 # C3-O3-C2-C4 1 0 5 2 2 # C5-C3-O4-C4 11 1 3 2 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME KA4 # -4-D-galactopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 1 2 # C4-O4-C3-C5 1 0 2 11 2 # C4-C6-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 1 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME KA6 # -6-D-galactopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 8 2 # C5-C3-O4-C4 11 2 9 8 2 # C4-C6-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 0 1 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 0 1 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 0 1 11 8 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CKA # # terminal -C1-O1-C1'(KA) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type KA # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C4'-O4'-C3'-C5' 8 9 11 7 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 3 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 35 # # terms of type : C4'-C5'-C6'-O6' (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # C4'-C5'-C6'-O6' 8 7 17 18 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME KB2 # -2-D-galactopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 1 12 14 13 2 # C2-O2-C3-C1 1 0 5 13 2 # C4-C2-O3-C3 2 1 6 5 2 # C4-O4-C3-C5 2 3 5 11 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME KB3 # -3-D-galactopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 1 6 5 2 # C3-O3-C2-C4 1 0 5 2 2 # C5-C3-O4-C4 11 1 3 2 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME KB4 # -4-D-galactopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 1 2 # C4-O4-C3-C5 1 0 2 11 2 # C4-C6-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 1 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME KB6 # -6-D-galactopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 8 2 # C5-C3-O4-C4 11 2 9 8 2 # C4-C6-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 0 1 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 0 1 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 0 1 11 8 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CKB # # terminal -C1-O1-C1'(KB) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type KB # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1'-O1-O5'-C2' 5 4 6 14 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C4'-O4'-C3'-C5' 8 9 11 7 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 3 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 35 # # terms of type : C4'-C5'-C6'-O6' (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # C4'-C5'-C6'-O6' 8 7 17 18 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 2 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 32 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME TA2 # -2-D-talopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 1 2 # C1-O2-C3-C2 13 0 5 1 2 # C4-C2-O3-C3 2 1 6 5 2 # C4-O4-C3-C5 2 3 5 11 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME TA3 # -3-D-talopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 1 6 13 2 # C3-O3-C2-C4 1 0 5 2 2 # C5-C3-O4-C4 11 1 3 2 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME TA4 # -4-D-talopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 2 6 13 2 # C3-O3-C2-C4 2 3 5 1 2 # C4-O4-C3-C5 1 0 2 11 2 # C4-C6-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 1 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME TA6 # -6-D-talopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 2 6 13 2 # C3-O3-C2-C4 2 3 5 8 2 # C5-C3-O4-C4 11 2 9 8 2 # C4-C6-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 0 1 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 0 1 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 0 1 11 8 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CTA # # terminal -C1-O1-C1'(TA) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type TA # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C2'-C3'-O2'-C1' 14 11 15 5 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C4'-O4'-C3'-C5' 8 9 11 7 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 3 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 35 # # terms of type : C4'-C5'-C6'-O6' (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # C4'-C5'-C6'-O6' 8 7 17 18 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME TB2 # -2-D-talopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 1 12 14 13 2 # C1-O2-C3-C2 13 0 5 1 2 # C4-C2-O3-C3 2 1 6 5 2 # C4-O4-C3-C5 2 3 5 11 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME TB3 # -3-D-talopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 1 6 13 2 # C3-O3-C2-C4 1 0 5 2 2 # C5-C3-O4-C4 11 1 3 2 2 # C4-C6-O5-C5 2 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME TB4 # -4-D-talopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 2 6 13 2 # C3-O3-C2-C4 2 3 5 1 2 # C4-O4-C3-C5 1 0 2 11 2 # C4-C6-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 1 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME TB6 # -6-D-talopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 2 6 13 2 # C3-O3-C2-C4 2 3 5 8 2 # C5-C3-O4-C4 11 2 9 8 2 # C4-C6-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 0 1 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 0 1 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 0 1 11 8 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CTB # # terminal -C1-O1-C1'(TB) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type TB # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1'-O1-O5'-C2' 5 4 6 14 2 # C2'-C3'-O2'-C1' 14 11 15 5 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C4'-O4'-C3'-C5' 8 9 11 7 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 3 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 35 # # terms of type : C4'-C5'-C6'-O6' (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # C4'-C5'-C6'-O6' 8 7 17 18 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 2 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 32 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME BA2 # -2-L-allopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 1 12 14 13 2 # C1-O2-C3-C2 13 0 5 1 2 # C4-C2-O3-C3 2 1 6 5 2 # C4-O4-C3-C5 2 3 5 11 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME BA3 # -3-L-allopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 1 6 13 2 # C3-O3-C2-C4 1 0 5 2 2 # C5-C3-O4-C4 11 1 3 2 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME BA4 # -4-L-allopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 2 6 13 2 # C3-O3-C2-C4 2 3 5 1 2 # C4-O4-C3-C5 1 0 2 11 2 # C5-C6-O5-C4 11 8 12 1 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME BA6 # -6-L-allopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 2 6 13 2 # C3-O3-C2-C4 2 3 5 8 2 # C5-C3-O4-C4 11 2 9 8 2 # C5-C6-O5-C4 11 1 12 8 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 0 1 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 0 1 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CBA # # terminal -C1-O1-C1'(BA) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type BA # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1'-O1-O5'-C2' 5 4 6 14 2 # C2'-C3'-O2'-C1' 14 11 15 5 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C4'-O4'-C3'-C5' 8 9 11 7 2 # C4'-O5'-C6'-C5' 8 6 17 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME BB2 # -2-L-allopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 1 2 # C1-O2-C3-C2 13 0 5 1 2 # C4-C2-O3-C3 2 1 6 5 2 # C4-O4-C3-C5 2 3 5 11 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME BB3 # -3-L-allopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 1 6 13 2 # C3-O3-C2-C4 1 0 5 2 2 # C5-C3-O4-C4 11 1 3 2 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME BB4 # -4-L-allopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 2 6 13 2 # C3-O3-C2-C4 2 3 5 1 2 # C4-O4-C3-C5 1 0 2 11 2 # C5-C6-O5-C4 11 8 12 1 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME BB6 # -6-L-allopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 2 6 13 2 # C3-O3-C2-C4 2 3 5 8 2 # C5-C3-O4-C4 11 2 9 8 2 # C5-C6-O5-C4 11 1 12 8 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 0 1 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 0 1 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CBB # # terminal -C1-O1-C1'(BB) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type BB # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C2'-C3'-O2'-C1' 14 11 15 5 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C4'-O4'-C3'-C5' 8 9 11 7 2 # C4'-O5'-C6'-C5' 8 6 17 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 2 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 32 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME SA2 # -2-L-altropyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 1 12 14 13 2 # C2-O2-C3-C1 1 0 5 13 2 # C4-C2-O3-C3 2 1 6 5 2 # C4-O4-C3-C5 2 3 5 11 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME SA3 # -3-L-altropyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 1 6 5 2 # C3-O3-C2-C4 1 0 5 2 2 # C5-C3-O4-C4 11 1 3 2 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME SA4 # -4-L-altropyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 1 2 # C4-O4-C3-C5 1 0 2 11 2 # C5-C6-O5-C4 11 8 12 1 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME SA6 # -6-L-altropyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 8 2 # C5-C3-O4-C4 11 2 9 8 2 # C5-C6-O5-C4 11 1 12 8 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 0 1 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 0 1 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CSA # # terminal -C1-O1-C1'(SA) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type SA # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1'-O1-O5'-C2' 5 4 6 14 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C4'-O4'-C3'-C5' 8 9 11 7 2 # C4'-O5'-C6'-C5' 8 6 17 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME SB2 # -2-L-altropyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 1 2 # C2-O2-C3-C1 1 0 5 13 2 # C4-C2-O3-C3 2 1 6 5 2 # C4-O4-C3-C5 2 3 5 11 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME SB3 # -3-L-altropyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 1 6 5 2 # C3-O3-C2-C4 1 0 5 2 2 # C5-C3-O4-C4 11 1 3 2 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME SB4 # -4-L-altropyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 1 2 # C4-O4-C3-C5 1 0 2 11 2 # C5-C6-O5-C4 11 8 12 1 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME SB6 # -6-L-altropyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 8 2 # C5-C3-O4-C4 11 2 9 8 2 # C5-C6-O5-C4 11 1 12 8 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 0 1 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 0 1 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CSB # # terminal -C1-O1-C1'(SB) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type SB # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C4'-O4'-C3'-C5' 8 9 11 7 2 # C4'-O5'-C6'-C5' 8 6 17 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 2 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 32 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME HA2 # -2-L-glucopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 1 12 14 13 2 # C1-O2-C3-C2 13 0 5 1 2 # C3-C2-O3-C4 5 1 6 2 2 # C4-O4-C3-C5 2 3 5 11 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME HA3 # -3-L-glucopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 1 6 13 2 # C4-O3-C2-C3 2 0 5 1 2 # C5-C3-O4-C4 11 1 3 2 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME HA4 # -4-L-glucopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 2 6 13 2 # C4-O3-C2-C3 1 3 5 2 2 # C4-O4-C3-C5 1 0 2 11 2 # C5-C6-O5-C4 11 8 12 1 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME HA6 # -6-L-glucopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 2 6 13 2 # C4-O3-C2-C3 8 3 5 2 2 # C5-C3-O4-C4 11 2 9 8 2 # C5-C6-O5-C4 11 1 12 8 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 0 1 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 0 1 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CHA # # terminal -C1-O1-C1'(HA) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type HA # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1'-O1-O5'-C2' 5 4 6 14 2 # C2'-C3'-O2'-C1' 14 11 15 5 2 # C4'-O3'-C2'-C3' 8 12 14 11 2 # C4'-O4'-C3'-C5' 8 9 11 7 2 # C4'-O5'-C6'-C5' 8 6 17 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME HB2 # -2-L-glucopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 1 2 # C1-O2-C3-C2 13 0 5 1 2 # C3-C2-O3-C4 5 1 6 2 2 # C4-O4-C3-C5 2 3 5 11 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME HB3 # -3-L-glucopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 1 6 13 2 # C4-O3-C2-C3 2 0 5 1 2 # C5-C3-O4-C4 11 1 3 2 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME HB4 # -4-L-glucopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 2 6 13 2 # C4-O3-C2-C3 1 3 5 2 2 # C4-O4-C3-C5 1 0 2 11 2 # C5-C6-O5-C4 11 8 12 1 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME HB6 # -6-L-glucopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 2 6 13 2 # C4-O3-C2-C3 8 3 5 2 2 # C5-C3-O4-C4 11 2 9 8 2 # C5-C6-O5-C4 11 1 12 8 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 0 1 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 0 1 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CHB # # terminal -C1-O1-C1'(HB) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type HB # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C2'-C3'-O2'-C1' 14 11 15 5 2 # C4'-O3'-C2'-C3' 8 12 14 11 2 # C4'-O4'-C3'-C5' 8 9 11 7 2 # C4'-O5'-C6'-C5' 8 6 17 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 2 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 32 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME NA2 # -2-L-mannopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 1 12 14 13 2 # C2-O2-C3-C1 1 0 5 13 2 # C3-C2-O3-C4 5 1 6 2 2 # C4-O4-C3-C5 2 3 5 11 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME NA3 # -3-L-mannopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 1 6 5 2 # C4-O3-C2-C3 2 0 5 1 2 # C5-C3-O4-C4 11 1 3 2 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME NA4 # -4-L-mannopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 2 6 5 2 # C4-O3-C2-C3 1 3 5 2 2 # C4-O4-C3-C5 1 0 2 11 2 # C5-C6-O5-C4 11 8 12 1 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME NA6 # -6-L-mannopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 2 6 5 2 # C4-O3-C2-C3 8 3 5 2 2 # C5-C3-O4-C4 11 2 9 8 2 # C5-C6-O5-C4 11 1 12 8 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 0 1 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 0 1 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CNA # # terminal -C1-O1-C1'(NA) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type NA # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1'-O1-O5'-C2' 5 4 6 14 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C4'-O3'-C2'-C3' 8 12 14 11 2 # C4'-O4'-C3'-C5' 8 9 11 7 2 # C4'-O5'-C6'-C5' 8 6 17 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME NB2 # -2-L-mannopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 1 2 # C2-O2-C3-C1 1 0 5 13 2 # C3-C2-O3-C4 5 1 6 2 2 # C4-O4-C3-C5 2 3 5 11 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME NB3 # -3-L-mannopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 1 6 5 2 # C4-O3-C2-C3 2 0 5 1 2 # C5-C3-O4-C4 11 1 3 2 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME NB4 # -4-L-mannopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 2 6 5 2 # C4-O3-C2-C3 1 3 5 2 2 # C4-O4-C3-C5 1 0 2 11 2 # C5-C6-O5-C4 11 8 12 1 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 9 8 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 9 8 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME NB6 # -6-L-mannopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 2 6 5 2 # C4-O3-C2-C3 8 3 5 2 2 # C5-C3-O4-C4 11 2 9 8 2 # C5-C6-O5-C4 11 1 12 8 2 # # --- dihedrals --- # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O6-C6-C5-O5 0 1 11 12 5 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O6-C6-C5-O5 0 1 11 12 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CNB # # terminal -C1-O1-C1'(NB) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type NB # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C4'-O3'-C2'-C3' 8 12 14 11 2 # C4'-O4'-C3'-C5' 8 9 11 7 2 # C4'-O5'-C6'-C5' 8 6 17 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 2 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 32 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME ZA2 # -2-L-gulopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 1 12 14 13 2 # C1-O2-C3-C2 13 0 5 1 2 # C4-C2-O3-C3 2 1 6 5 2 # C5-O4-C3-C4 11 3 5 2 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME ZA3 # -3-L-gulopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 1 6 13 2 # C3-O3-C2-C4 1 0 5 2 2 # C4-C3-O4-C5 2 1 3 11 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME ZA4 # -4-L-gulopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 2 6 13 2 # C3-O3-C2-C4 2 3 5 1 2 # C5-O4-C3-C4 11 0 2 1 2 # C5-C6-O5-C4 11 8 12 1 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 1 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME ZA6 # -6-L-gulopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 2 6 13 2 # C3-O3-C2-C4 2 3 5 8 2 # C4-C3-O4-C5 8 2 9 11 2 # C5-C6-O5-C4 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 0 1 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 0 1 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 0 1 11 8 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CZA # # terminal -C1-O1-C1'(ZA) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type ZA # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1'-O1-O5'-C2' 5 4 6 14 2 # C2'-C3'-O2'-C1' 14 11 15 5 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C4'-O5'-C6'-C5' 8 6 17 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 3 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 35 # # terms of type : C4'-C5'-C6'-O6' (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # C4'-C5'-C6'-O6' 8 7 17 18 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME ZB2 # -2-L-gulopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 1 2 # C1-O2-C3-C2 13 0 5 1 2 # C4-C2-O3-C3 2 1 6 5 2 # C5-O4-C3-C4 11 3 5 2 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME ZB3 # -3-L-gulopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 1 6 13 2 # C3-O3-C2-C4 1 0 5 2 2 # C4-C3-O4-C5 2 1 3 11 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME ZB4 # -4-L-gulopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 2 6 13 2 # C3-O3-C2-C4 2 3 5 1 2 # C5-O4-C3-C4 11 0 2 1 2 # C5-C6-O5-C4 11 8 12 1 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 1 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME ZB6 # -6-L-gulopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 2 6 13 2 # C3-O3-C2-C4 2 3 5 8 2 # C4-C3-O4-C5 8 2 9 11 2 # C5-C6-O5-C4 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 0 1 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 0 1 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 0 1 11 8 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CZB # # terminal -C1-O1-C1'(ZB) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type ZB # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C2'-C3'-O2'-C1' 14 11 15 5 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C4'-O5'-C6'-C5' 8 6 17 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 3 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 35 # # terms of type : C4'-C5'-C6'-O6' (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # C4'-C5'-C6'-O6' 8 7 17 18 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 2 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 32 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME JA2 # -2-L-idopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 1 12 14 13 2 # C2-O2-C3-C1 1 0 5 13 2 # C4-C2-O3-C3 2 1 6 5 2 # C5-O4-C3-C4 11 3 5 2 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME JA3 # -3-L-idopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 1 6 5 2 # C3-O3-C2-C4 1 0 5 2 2 # C4-C3-O4-C5 2 1 3 11 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME JA4 # -4-L-idopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 1 2 # C5-O4-C3-C4 11 0 2 1 2 # C5-C6-O5-C4 11 8 12 1 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 1 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME JA6 # -6-L-idopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 8 2 # C4-C3-O4-C5 8 2 9 11 2 # C5-C6-O5-C4 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 0 1 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 0 1 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 0 1 11 8 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CJA # # terminal -C1-O1-C1'(JA) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type JA # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1'-O1-O5'-C2' 5 4 6 14 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C4'-O5'-C6'-C5' 8 6 17 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 3 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 35 # # terms of type : C4'-C5'-C6'-O6' (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # C4'-C5'-C6'-O6' 8 7 17 18 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME JB2 # -2-L-idopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 1 2 # C2-O2-C3-C1 1 0 5 13 2 # C4-C2-O3-C3 2 1 6 5 2 # C5-O4-C3-C4 11 3 5 2 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME JB3 # -3-L-idopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 1 6 5 2 # C3-O3-C2-C4 1 0 5 2 2 # C4-C3-O4-C5 2 1 3 11 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME JB4 # -4-L-idopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 1 2 # C5-O4-C3-C4 11 0 2 1 2 # C5-C6-O5-C4 11 8 12 1 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 1 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME JB6 # -6-L-idopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 8 2 # C4-C3-O4-C5 8 2 9 11 2 # C5-C6-O5-C4 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 0 1 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 0 1 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 0 1 11 8 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CJB # # terminal -C1-O1-C1'(JB) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type JB # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C4'-O5'-C6'-C5' 8 6 17 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 3 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 35 # # terms of type : C4'-C5'-C6'-O6' (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # C4'-C5'-C6'-O6' 8 7 17 18 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 2 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 32 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME LA2 # -2-L-galactopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 1 12 14 13 2 # C1-O2-C3-C2 13 0 5 1 2 # C3-C2-O3-C4 5 1 6 2 2 # C5-O4-C3-C4 11 3 5 2 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME LA3 # -3-L-galactopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 1 6 13 2 # C4-O3-C2-C3 2 0 5 1 2 # C4-C3-O4-C5 2 1 3 11 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME LA4 # -4-L-galactopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 2 6 13 2 # C4-O3-C2-C3 1 3 5 2 2 # C5-O4-C3-C4 11 0 2 1 2 # C5-C6-O5-C4 11 8 12 1 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 1 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME LA6 # -6-L-galactopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 2 6 13 2 # C4-O3-C2-C3 8 3 5 2 2 # C4-C3-O4-C5 8 2 9 11 2 # C5-C6-O5-C4 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 0 1 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 0 1 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 0 1 11 8 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CLA # # terminal -C1-O1-C1'(LA) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type LA # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1'-O1-O5'-C2' 5 4 6 14 2 # C2'-C3'-O2'-C1' 14 11 15 5 2 # C4'-O3'-C2'-C3' 8 12 14 11 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C4'-O5'-C6'-C5' 8 6 17 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 3 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 35 # # terms of type : C4'-C5'-C6'-O6' (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # C4'-C5'-C6'-O6' 8 7 17 18 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME LB2 # -2-L-galactopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 1 2 # C1-O2-C3-C2 13 0 5 1 2 # C3-C2-O3-C4 5 1 6 2 2 # C5-O4-C3-C4 11 3 5 2 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME LB3 # -3-L-galactopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 1 6 13 2 # C4-O3-C2-C3 2 0 5 1 2 # C4-C3-O4-C5 2 1 3 11 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME LB4 # -4-L-galactopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 2 6 13 2 # C4-O3-C2-C3 1 3 5 2 2 # C5-O4-C3-C4 11 0 2 1 2 # C5-C6-O5-C4 11 8 12 1 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 1 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME LB6 # -6-L-galactopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C2-C3-O2-C1 5 2 6 13 2 # C4-O3-C2-C3 8 3 5 2 2 # C4-C3-O4-C5 8 2 9 11 2 # C5-C6-O5-C4 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 0 1 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 0 1 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 0 1 11 8 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CLB # # terminal -C1-O1-C1'(LB) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type LB # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C2'-C3'-O2'-C1' 14 11 15 5 2 # C4'-O3'-C2'-C3' 8 12 14 11 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C4'-O5'-C6'-C5' 8 6 17 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 3 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 35 # # terms of type : C4'-C5'-C6'-O6' (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # C4'-C5'-C6'-O6' 8 7 17 18 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 2 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 32 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME UA2 # -2-L-talopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 1 12 14 13 2 # C2-O2-C3-C1 1 0 5 13 2 # C3-C2-O3-C4 5 1 6 2 2 # C5-O4-C3-C4 11 3 5 2 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME UA3 # -3-L-talopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 1 6 5 2 # C4-O3-C2-C3 2 0 5 1 2 # C4-C3-O4-C5 2 1 3 11 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME UA4 # -4-L-talopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 2 6 5 2 # C4-O3-C2-C3 1 3 5 2 2 # C5-O4-C3-C4 11 0 2 1 2 # C5-C6-O5-C4 11 8 12 1 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 1 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME UA6 # -6-L-talopyranose-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 2 6 5 2 # C4-O3-C2-C3 8 3 5 2 2 # C4-C3-O4-C5 8 2 9 11 2 # C5-C6-O5-C4 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 0 1 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 0 1 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 0 1 11 8 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CUA # # terminal -C1-O1-C1'(UA) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type UA # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1'-O1-O5'-C2' 5 4 6 14 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C4'-O3'-C2'-C3' 8 12 14 11 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C4'-O5'-C6'-C5' 8 6 17 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 3 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 35 # # terms of type : C4'-C5'-C6'-O6' (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # C4'-C5'-C6'-O6' 8 7 17 18 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(2:1) # building block (residue, nucleotide, etc.) # RNME UB2 # -2-L-talopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch C2OH (HO2, O2)] # the C1_prev-O2 and O2-C2 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 14 3 0.23200 1 6 2 5 6 12 13 14 2 C4 14 3 0.23200 0 7 3 4 5 6 8 11 12 3 O4 3 16 -0.64200 0 3 4 5 11 4 HO4 21 1 0.41000 1 0 5 C3 14 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 2 5 26 # C4-C5 2 11 26 # C2-C3 1 5 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O3-HO3 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 2 11 8 # C2-C3-C4 1 5 2 8 # C3-C2-C1 5 1 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 3 2 5 9 # O4-C4-C5 3 2 11 9 # C4-C3-O3 2 5 6 9 # C2-C3-O3 1 5 6 9 # O2-C2-C3 0 1 5 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 1 2 # C2-O2-C3-C1 1 0 5 13 2 # C3-C2-O3-C4 5 1 6 2 2 # C5-O4-C3-C4 11 3 5 2 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 1 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 0 1 13 14 18 # O2-C2-C3-O3 0 1 5 6 18 # O4-C4-C3-O3 3 2 5 6 18 # # terms of type : C-C-C-C formed by ring atoms # # C1-C2-C3-C4 13 1 5 2 34 # C5-C4-C3-C2 11 2 5 1 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 5 1 13 12 34 # C3-C4-C5-O5 5 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 5 1 13 14 17 # O2-C2-C3-C4 0 1 5 2 17 # C1-C2-C3-O3 13 1 5 6 17 # C5-C4-C3-O3 11 2 5 6 17 # O4-C4-C3-C2 3 2 5 1 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 5 1 13 12 17 # C3-C4-C5-O5 5 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C2-C3-O3-HO3 1 5 6 7 30 # C3-C4-O4-HO4 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O2-C2-C1 -1 0 1 13 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(3:1) # building block (residue, nucleotide, etc.) # RNME UB3 # -3-L-talopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch C3OH (HO3, O3)] # the C1_prev-O3 and O3-C3 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 14 3 0.23200 1 6 2 3 5 6 11 13 2 C4 14 3 0.23200 0 6 3 4 5 8 11 12 3 O4 3 16 -0.64200 0 2 4 11 4 HO4 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 2 26 # C4-C5 2 11 26 # C3-C2 1 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C4-O4 2 3 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O4-HO4 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 2 11 8 # C4-C3-C2 2 1 5 8 # C3-C2-C1 1 5 13 8 # C4-C5-C6 2 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 2 3 9 # O4-C4-C5 3 2 11 9 # O3-C3-C4 0 1 2 9 # O3-C3-C2 0 1 5 9 # C3-C2-O2 1 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 2 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C4-O4-HO4 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 1 6 5 2 # C4-O3-C2-C3 2 0 5 1 2 # C4-C3-O4-C5 2 1 3 11 2 # C5-C6-O5-C4 11 8 12 2 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 2 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 0 1 5 6 18 # O3-C3-C4-O4 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 2 1 5 13 34 # C2-C3-C4-C5 5 1 2 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 1 5 13 12 34 # C3-C4-C5-O5 1 2 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 1 5 13 14 17 # C4-C3-C2-O2 2 1 5 6 17 # O3-C3-C2-C1 0 1 5 13 17 # O3-C3-C4-C5 0 1 2 11 17 # C2-C3-C4-O4 5 1 2 3 17 # O4-C4-C5-C6 3 2 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 1 5 13 12 17 # C3-C4-C5-O5 1 2 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 2 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C3-C4-O4-HO4 1 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O3-C3-C2 -1 0 1 5 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(4:1) # building block (residue, nucleotide, etc.) # RNME UB4 # -4-L-talopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 2 6 5 2 # C4-O3-C2-C3 1 3 5 2 2 # C5-O4-C3-C4 11 0 2 1 2 # C5-C6-O5-C4 11 8 12 1 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 9 8 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 9 8 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 9 8 11 1 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C5-C6-O6-HO6 11 8 9 10 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXP(6:1) # building block (residue, nucleotide, etc.) # RNME UB6 # -6-L-talopyranose-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch C6OH (HO6, O6)] # the C1_prev-O6 and O6-C6 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C3 14 3 0.23200 0 8 3 4 5 6 8 9 11 13 3 O3 3 16 -0.64200 0 3 4 5 8 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 6 6 7 8 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C4 14 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 8 26 # C4-C5 8 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 8 11 8 # C2-C3-C4 5 2 8 8 # C3-C2-C1 2 5 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 3 2 8 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 2 6 5 2 # C4-O3-C2-C3 8 3 5 2 2 # C4-C3-O4-C5 8 2 9 11 2 # C5-C6-O5-C4 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 8 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O3-C3-C4-O4 3 2 8 9 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 8 2 5 13 34 # C2-C3-C4-C5 5 2 8 11 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 8 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 8 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # O3-C3-C4-C5 3 2 8 11 17 # C2-C3-C4-O4 5 2 8 9 17 # O4-C4-C5-C6 9 8 11 1 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 8 11 12 17 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-O5 0 1 11 12 3 # # terms of type : O5-C5-C6-O6 (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O6-C6-C5-O5 0 1 11 12 35 # # terms of type : C4-C5-C6-O6 (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # O6-C6-C5-C4 0 1 11 8 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C3-C4-O4-HO4 2 8 9 10 30 # C1_prev-O6-C6-C5 -1 0 1 11 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME CUB # # terminal -C1-O1-C1'(UB) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional pyranose residue of type UB # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 5 8 9 11 17 18 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C4'-O3'-C2'-C3' 8 12 14 11 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C4'-O5'-C6'-C5' 8 6 17 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 26 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 3 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with syn C4,C5 as in Gal (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 18 35 # # terms of type : C4'-C5'-C6'-O6' (omega dihedral) specific to residue with syn C4,C5 as in Gal (1-fold term) # # C4'-C5'-C6'-O6' 8 7 17 18 1 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # C5'-C6'-O6'-HO6' 7 17 18 19 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 2 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 32 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXU(4:1) # building block (residue, nucleotide, etc.) # RNME GB4U # -4-D-glucuronate-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 12 12 0.72000 0 4 9 10 11 12 9 O61 2 16 -0.36000 0 2 10 11 10 O62 2 16 -0.36000 1 1 11 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # # terms of type : C-C(carboxylate) # # C6-C5 8 11 27 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O(carboxylate) # # C6-O61 8 9 6 # C6-O62 8 10 6 # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # # --- bond angles --- # # NBA 22 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O(carboxylate) # # O61-C6-C5 9 8 11 22 # O62-C6-C5 10 8 11 22 # # terms of type : O-C-O(carboxylate) # # O61-C6-O62 9 8 10 38 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # # --- improper dihedrals --- # # NIDA 6 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 1 2 # C5-O4-C3-C4 11 0 2 1 2 # C4-C6-O5-C5 1 8 12 11 2 # # terms of type : planar geometry around C6 (carboxylate group) # # C6-O61-O62-C5 8 9 10 11 1 # # --- dihedrals --- # # NDA 23 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O61 (gamma-tilde dihedral) for carboxylate # # O61-C6-C5-O5 9 8 11 12 40 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXU(1:-) # building block (residue, nucleotide, etc.) # RNME UGB # # terminal -C1-O1-C1'(GBU) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional uronate residue of type GBU # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 4 8 9 11 17 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 12 12 0.72000 0 0 18 O61' 2 16 -0.36000 0 0 19 O62' 2 16 -0.36000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # O6'-C6' 0 17 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 0 0 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # O6'-C6'-C5' 0 17 7 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # HO6'-O6'-C6' 0 0 17 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1'-O1-O5'-C2' 5 4 6 14 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 0 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 0 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # HO6'-O6'-C6'-C5' 0 0 17 7 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 2 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 32 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXU(4:1) # building block (residue, nucleotide, etc.) # RNME KA4U # -4-D-galacturonate-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 12 12 0.72000 0 4 9 10 11 12 9 O61 2 16 -0.36000 0 2 10 11 10 O62 2 16 -0.36000 1 1 11 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # # terms of type : C-C(carboxylate) # # C6-C5 8 11 27 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O(carboxylate) # # C6-O61 8 9 6 # C6-O62 8 10 6 # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # # --- bond angles --- # # NBA 22 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O(carboxylate) # # O61-C6-C5 9 8 11 22 # O62-C6-C5 10 8 11 22 # # terms of type : O-C-O(carboxylate) # # O61-C6-O62 9 8 10 38 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # # --- improper dihedrals --- # # NIDA 6 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1-O5-O1-C2 13 12 14 5 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 1 2 # C4-O4-C3-C5 1 0 2 11 2 # C4-C6-O5-C5 1 8 12 11 2 # # terms of type : planar geometry around C6 (carboxylate group) # # C6-O61-O62-C5 8 9 10 11 1 # # --- dihedrals --- # # NDA 23 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O61 (gamma-tilde dihedral) for carboxylate # # O61-C6-C5-O5 9 8 11 12 40 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXU(1:-) # building block (residue, nucleotide, etc.) # RNME UKA # # terminal -C1-O1-C1'(KAU) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional uronate residue of type KAU # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 4 8 9 11 17 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 12 12 0.72000 0 0 18 O61' 2 16 -0.36000 0 0 19 O62' 2 16 -0.36000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # O6'-C6' 0 17 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 0 0 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # O6'-C6'-C5' 0 17 7 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # HO6'-O6'-C6' 0 0 17 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 0 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 0 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # HO6'-O6'-C6'-C5' 0 0 17 7 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXU(4:1) # building block (residue, nucleotide, etc.) # RNME MB4U # -4-D-mannuronate-beta-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 12 12 0.72000 0 4 9 10 11 12 9 O61 2 16 -0.36000 0 2 10 11 10 O62 2 16 -0.36000 1 1 11 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # # terms of type : C-C(carboxylate) # # C6-C5 8 11 27 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O(carboxylate) # # C6-O61 8 9 6 # C6-O62 8 10 6 # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # # --- bond angles --- # # NBA 22 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O(carboxylate) # # O61-C6-C5 9 8 11 22 # O62-C6-C5 10 8 11 22 # # terms of type : O-C-O(carboxylate) # # O61-C6-O62 9 8 10 38 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # # --- improper dihedrals --- # # NIDA 6 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 2 6 13 2 # C3-O3-C2-C4 2 3 5 1 2 # C5-O4-C3-C4 11 0 2 1 2 # C4-C6-O5-C5 1 8 12 11 2 # # terms of type : planar geometry around C6 (carboxylate group) # # C6-O61-O62-C5 8 9 10 11 1 # # --- dihedrals --- # # NDA 23 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O61 (gamma-tilde dihedral) for carboxylate # # O61-C6-C5-O5 9 8 11 12 40 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 2 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for beta anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 32 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXU(1:-) # building block (residue, nucleotide, etc.) # RNME UMB # # terminal -C1-O1-C1'(MBU) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional uronate residue of type MBU # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 4 8 9 11 17 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 12 12 0.72000 0 0 18 O61' 2 16 -0.36000 0 0 19 O62' 2 16 -0.36000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # O6'-C6' 0 17 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 0 0 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # O6'-C6'-C5' 0 17 7 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # HO6'-O6'-C6' 0 0 17 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C1'-O1-O5'-C2' 5 4 6 14 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 0 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 0 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # HO6'-O6'-C6'-C5' 0 0 17 7 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 2 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for beta anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 32 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXU(4:1) # building block (residue, nucleotide, etc.) # RNME ZA4U # -4-L-guluronate-alpha-1 # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 12 12 0.72000 0 4 9 10 11 12 9 O61 2 16 -0.36000 0 2 10 11 10 O62 2 16 -0.36000 1 1 11 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # # terms of type : C-C(carboxylate) # # C6-C5 8 11 27 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O(carboxylate) # # C6-O61 8 9 6 # C6-O62 8 10 6 # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # # --- bond angles --- # # NBA 22 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O(carboxylate) # # O61-C6-C5 9 8 11 22 # O62-C6-C5 10 8 11 22 # # terms of type : O-C-O(carboxylate) # # O61-C6-O62 9 8 10 38 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # # --- improper dihedrals --- # # NIDA 6 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C2-C3-O2-C1 5 2 6 13 2 # C3-O3-C2-C4 2 3 5 1 2 # C5-O4-C3-C4 11 0 2 1 2 # C5-C6-O5-C4 11 8 12 1 2 # # terms of type : planar geometry around C6 (carboxylate group) # # C6-O61-O62-C5 8 9 10 11 1 # # --- dihedrals --- # # NDA 23 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O61 (gamma-tilde dihedral) for carboxylate # # O61-C6-C5-O5 9 8 11 12 40 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXU(1:-) # building block (residue, nucleotide, etc.) # RNME UZA # # terminal -C1-O1-C1'(ZAU) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional uronate residue of type ZAU # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 4 8 9 11 17 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 12 12 0.72000 0 0 18 O61' 2 16 -0.36000 0 0 19 O62' 2 16 -0.36000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # O6'-C6' 0 17 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 0 0 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # O6'-C6'-C5' 0 17 7 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # HO6'-O6'-C6' 0 0 17 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 0 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 0 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # HO6'-O6'-C6'-C5' 0 0 17 7 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE _carbo SOL RESID HEXU(4:1) # building block (residue, nucleotide, etc.) # RNME JA4U # -4-L-iduronate-alpha-1- # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch C4OH (HO4, O4)] # the C1_prev-O4 and O4-C4 bonds are *not* defined in the residue (but in the prev) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 14 3 0.23200 1 6 2 3 5 8 11 12 2 C3 14 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C2 14 3 0.23200 0 5 6 7 12 13 14 6 O2 3 16 -0.64200 0 2 7 13 7 HO2 21 1 0.41000 1 0 8 C6 12 12 0.72000 0 4 9 10 11 12 9 O61 2 16 -0.36000 0 2 10 11 10 O62 2 16 -0.36000 1 1 11 11 C5 14 3 0.37600 0 2 12 13 12 O5 3 16 -0.48000 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1-O1 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 14 3 0.23200 0 14 O1 3 16 -0.36000 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 2 26 # C4-C5 1 11 26 # C3-C2 2 5 26 # C2-C1 5 13 26 # # terms of type : C-C(carboxylate) # # C6-C5 8 11 27 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next 14 15 20 # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 5 6 20 # C3-O3 2 3 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O(carboxylate) # # C6-O61 8 9 6 # C6-O62 8 10 6 # # terms of type : O-H # # O2-HO2 6 7 1 # O3-HO3 3 4 1 # # --- bond angles --- # # NBA 22 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 1 11 8 # C4-C3-C2 1 2 5 8 # C3-C2-C1 2 5 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O(carboxylate) # # O61-C6-C5 9 8 11 22 # O62-C6-C5 10 8 11 22 # # terms of type : O-C-O(carboxylate) # # O61-C6-O62 9 8 10 38 # # terms of type : C-C-O # # O4-C4-C3 0 1 2 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 2 3 9 # O3-C3-C2 3 2 5 9 # C3-C2-O2 2 5 6 9 # O2-C2-C1 6 5 13 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 5 13 12 9 # C2-C1-O1 5 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 5 6 7 12 # C3-O3-HO3 2 3 4 12 # # --- improper dihedrals --- # # NIDA 6 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2-O5-O1-C1 5 12 14 13 2 # C1-C3-O2-C2 13 2 6 5 2 # C3-O3-C2-C4 2 3 5 1 2 # C5-O4-C3-C4 11 0 2 1 2 # C5-C6-O5-C4 11 8 12 1 2 # # terms of type : planar geometry around C6 (carboxylate group) # # C6-O61-O62-C5 8 9 10 11 1 # # --- dihedrals --- # # NDA 23 # IB JB KB LB MCB # # terms of type : C-C-O5-C formed by ring atoms # # C4-C5-O5-C1 1 11 12 13 29 # C5-O5-C1-C2 11 12 13 5 29 # # terms of type : O-C-C-O excluding O5 # # O2-C2-C1-O1 6 5 13 14 18 # O3-C3-C2-O2 3 2 5 6 18 # O4-C4-C3-O3 0 1 2 3 18 # # terms of type : C-C-C-C formed by ring atoms # # C4-C3-C2-C1 1 2 5 13 34 # C5-C4-C3-C2 11 1 2 5 34 # # terms of type : C-C-C-O5 formed by ring atoms (3-fold term) # # C3-C2-C1-O5 2 5 13 12 34 # C3-C4-C5-O5 2 1 11 12 34 # # terms of type : C-C-C-O excluding O5 and O6 # # C3-C2-C1-O1 2 5 13 14 17 # C4-C3-C2-O2 1 2 5 6 17 # O3-C3-C2-C1 3 2 5 13 17 # C5-C4-C3-O3 11 1 2 3 17 # O4-C4-C3-C2 0 1 2 5 17 # O4-C4-C5-C6 0 1 11 8 17 # # terms of type : C-C-C-O5 formed by ring atoms (2-fold term) # # C3-C2-C1-O5 2 5 13 12 17 # C3-C4-C5-O5 2 1 11 12 17 # # terms of type : O5-C5-C6-O61 (gamma-tilde dihedral) for carboxylate # # O61-C6-C5-O5 9 8 11 12 40 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals, including prev glycosidic psi dihedral) # # C1-C2-O2-HO2 13 5 6 7 30 # C2-C3-O3-HO3 5 2 3 4 30 # C1_prev-O4-C4-C3 -1 0 1 2 30 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (1-fold term) # # O5-C1-O1-C#_next 12 13 14 15 6 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : O5-C1-O1-C#_next (glycosidic phi dihedral) for alpha anomer (3-fold term) # # O5-C1-O1-C#_next 12 13 14 15 28 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXU(1:-) # building block (residue, nucleotide, etc.) # RNME UJA # # terminal -C1-O1-C1'(JAU) group for carbohydrates ending in a # trehalo 1-1' linkage to an additional uronate residue of type JAU # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond is *not* defined in the patch (but in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 14 3 0.37800 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.45000 0 2 3 4 # excluded: O1 and C1' 3 C1 14 3 0.24200 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 3 16 -0.34000 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 14 3 0.24200 0 5 6 7 11 14 15 6 O5' 3 16 -0.45000 0 4 7 8 14 17 7 C5' 14 3 0.37800 1 4 8 9 11 17 8 C4' 14 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 14 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 14 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 12 12 0.72000 0 0 18 O61' 2 16 -0.36000 0 0 19 O62' 2 16 -0.36000 1 0 # # --- bonds --- # (new or replacement) # # NB 15 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' # this term is skipped: already included appropriately in the patched residue # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # O6'-C6' 0 17 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 0 0 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # O6'-C6'-C5' 0 17 7 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # HO6'-O6'-C6' 0 0 17 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - the one neighbor to # the three other ones; the exocyclic atom is the 2nd or 3rd atom, depending on the chirality) # # C2'-O1-O5'-C1' 14 4 6 5 2 # C1'-C3'-O2'-C2' 5 11 15 14 2 # C3'-O3'-C2'-C4' 11 12 14 8 2 # C5'-O4'-C3'-C4' 7 9 11 8 2 # C5'-O5'-C6'-C4' 7 6 17 8 2 # # --- dihedrals --- # (new or replacement) # # NDA 25 # IB JB KB LB MCB # # terms of type : C-C-O5'-C formed by ring atoms # # C1'-O5'-C5'-C4' 5 6 7 8 29 # C2'-C1'-O5'-C5' 14 5 6 7 29 # # terms of type : O-C-C-O excluding O5 # # O1-C1'-C2'-O2' 4 5 14 15 18 # O3'-C3'-C2'-O2' 12 11 14 15 18 # O4'-C4'-C3'-O3' 9 8 11 12 18 # # terms of type : C-C-C-C formed by ring atoms # # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # # terms of type : C-C-C-O5' formed by ring atoms (3-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : C-C-C-O excluding O5'and O6 # # O1-C1'-C2'-C3' 4 5 14 11 17 # C4'-C3'-C2'-O2' 8 11 14 15 17 # O3'-C3'-C2'-C1' 12 11 14 5 17 # C5'-C4'-C3'-O3' 7 8 11 12 17 # O4'-C4'-C3'-C2' 9 8 11 14 17 # C6'-C5'-C4'-O4' 17 7 8 9 17 # # terms of type : C-C-C-O5' formed by ring atoms (2-fold term) # # O5'-C1'-C2'-C3' 6 5 14 11 17 # O5'-C5'-C4'-C3' 6 7 8 11 17 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (1-fold term) # # O5'-C5'-C6'-O6' 6 7 17 0 5 # # terms of type : O5'-C5'-C6'-O6' (omega-tilde dihedral) for residue with anti C4,C5 as in Glc (3-fold term) # # O5'-C5'-C6'-O6' 6 7 17 0 37 # # terms of type : C(n-1)-Cn-On-Hn with n=2,3,4,6 (chi dihedrals; no psi dihedral in a trehalo linkage) # # C1'-C2'-O2'-HO2' 5 14 15 16 30 # C2'-C3'-O3'-HO3' 14 11 12 13 30 # C3'-C4'-O4'-HO4' 11 8 9 10 30 # HO6'-O6'-C6'-C5' 0 0 17 7 30 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (1-fold term) # # C1-O1-C1'-O5' 3 4 5 6 6 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) # # terms of type : O5'-C1'-O1-C1 (glycosidic phi' dihedral) for alpha anomer (3-fold term) # # C1-O1-C1'-O5' 3 4 5 6 28 # O5-C1-O1-C1' # this term is skipped: already included appropriately in the patched residue (phi dihedral) #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME C1OC # # terminal -C1-O1-CH3 group for carbohydrates # # number of atoms, number of atoms to be replaced # NMAT NREP 3 -2 # # - the O1-CM bond is *not* defined in the patch (but in the residue) # - the C1-O1-CM angle is *not* defined in the patch (but in the residue) # - the O5-C1-O1-CM dihedral (phi dihedral) is *not* defined in the patch (but in the residue) # - the exclusions of C1, O1 and CM *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5 is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O1 and CM 1 C1 14 3 0.23200 0 2 2 3 # excluded: CM 2 O1 3 16 -0.36000 0 1 3 # # -- new atoms -- # (exclusions defined here) # 3 CM 16 5 0.23200 1 0 # # -- bonds -- # (new or replacement) # # NB 0 # IB JB MCB # C1-O1 and O1-CM skipped: already included appropriately in the patched residue # # -- bond angles -- # (new or replacement) # # NBA 0 # IB JB KB MCB # C1-O1-CM skipped: already included appropriately in the patched residue # # -- improper dihedrals -- # (new or replacement) # # NIDA 0 # IB JB KB LB MCB # # -- dihedrals -- # (new or replacement) # # NDA 0 # IB JB KB LB MCB # O5-C1-O1-CM skipped: already included appropriately in the patched residue # (same phi dihedral potential for all substitutions) #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo TER RESID HEXP(1:-) # building block (residue, nucleotide, etc.) # RNME C1OH # # terminal -C1-O1-HO1 group for carbohydrates # # number of atoms, number of atoms to be replaced # NMAT NREP 4 -3 # # - the O1-H1 bond *is* defined in the patch as a replacement # - the C1-O1-H1 angle *is* defined in the patch as a replacement # - the O5-C1-O1-H1 dihedral (phi dihedral) is *not* defined in the patch (but in the residue) # - the exclusions of O5, C1, O1 and HO1 *are* defined in the patch (replace those defined in the residue, # which are identical up to one exception: a special 1-4 exclusion [ring oxygen O5 to lactol hydrogen HO1] # specific to this force-field is introduced) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # excluded: C1, O1 and HO1 # the last one is a special 1-4 exclusion (ring oxygen to lactol hydrogen), specific to this force-field 1 O5 3 16 -0.48000 0 3 2 3 4 # excluded: O1 and HO1 2 C1 14 3 0.23200 0 2 3 4 # excluded: HO1 3 O1 3 16 -0.53800 0 1 4 # # -- new atoms -- # (exclusions defined here) # 4 HO1 21 1 0.41000 1 0 # # -- bonds -- # (new or replacement) # # NB 1 # IB JB MCB # O5-C1, C1-O1 skipped: already included appropriately in the patched residue # O1-HO1 (replacement) 3 4 1 # # -- bond angles -- # (new or replacement) # # NBA 1 # IB JB KB MCB # O5-C1-O1 skipped: already included appropriately in the patched residue # C1-O1-H1 (replacement) 2 3 4 12 # # -- improper dihedrals -- # (new or replacement) # # NIDA 0 # IB JB KB LB MCB # # -- dihedrals -- # (new or replacement) # # NDA 0 # IB JB KB LB MCB # O5-C1-O1-HO1 skipped: already included appropriately in the patched residue # (same phi dihedral potential for all substitutions) #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo INI RESID HEXP(-:2) # building block (residue, nucleotide, etc.) # RNME C2OH # # initial HO2-O2-C2- group for carbohydrates, to be used with a @*2 residue # # number of atoms, number of atoms to be replaced # NMAT NREP 3 1 # # - the HO2-O2 and O2-C2 bonds *are* defined in the patch # - the HO2-O2-C2 angle *is* defined in the patch # - the HO2-O2-C2-C1 (chi2 dihedral) is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the exclusions of HO2 and O2 *are* defined in the patch (replace those defined in the residue, which are identical) # - the exclusions of C2 are *not* defined in the patch (but in the residue) # # -- new atoms -- # (their exclusions replace those defined in the residue concerning preceding atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # excluded: O2 and C2 1 HO2 21 1 0.41000 0 2 2 3 # excluded: C2, C3 and C1 2 O2 3 16 -0.64200 0 3 3 7 15 # # -- replacement atoms -- # (exclusions defined in the residue) # 3 C2 14 3 0.23200 1 # # -- bonds -- # (new or replacement) # # NB 2 # IB JB MCB # HO2-O2 (new) 1 2 1 # C2-O2 (new) 2 3 20 # # -- bond angles -- # (new or replacement) # # NBA 1 # IB JB KB MCB # HO2-O2-C2 (new) 1 2 3 12 # # -- improper dihedrals -- # (new or replacement) # # NIDA 0 # IB JB KB LB MCB # # -- dihedrals -- # (new or replacement) # # NDA 0 # IB JB KB LB MCB # PHH, May 2011: the HO2-O2-C2-C1 dihedral was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo INI RESID HEXP(-:3) # building block (residue, nucleotide, etc.) # RNME C3OH # # initial HO3-O3-C3- group for carbohydrates, to be used with a @*3 residue # # number of atoms, number of atoms to be replaced # NMAT NREP 3 1 # # - the HO3-O3 and O3-C3 bonds *are* defined in the patch # - the HO3-O3-C3 angle *is* defined in the patch # - the HO3-O3-C3-C2 (chi3 dihedral) is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the exclusions of HO3 and O3 *are* defined in the patch (replace those defined in the residue, which are identical) # - the exclusions of C3 are *not* defined in the patch (but in the residue) # # -- new atoms -- # (their exclusions replace those defined in the residue concerning preceding atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # excluded: O3 and C3 1 HO3 21 1 0.41000 0 2 2 3 # excluded: C3, C4 and C2 2 O3 3 16 -0.64200 0 3 3 4 7 # # -- replacement atoms -- # (exclusions defined in the residue) # 3 C3 14 3 0.23200 1 # # -- bonds -- # (new or replacement) # # NB 2 # IB JB MCB # HO3-O3 (new) 1 2 1 # C3-O3 (new) 2 3 20 # # -- bond angles -- # (new or replacement) # # NBA 1 # IB JB KB MCB # HO3-O3-C3 (new) 1 2 3 12 # # -- improper dihedrals -- # (new or replacement) # # NIDA 0 # IB JB KB LB MCB # # -- dihedrals -- # (new or replacement) # # NDA 0 # IB JB KB LB MCB # PHH, May 2011: the HO3-O3-C3-C2 dihedral was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo INI RESID HEXP(-:4) # building block (residue, nucleotide, etc.) # RNME C4OH # # initial HO4-O4-C4- group for carbohydrates, to be used with a @*4 residue # # number of atoms, number of atoms to be replaced # NMAT NREP 3 1 # # - the HO4-O4 and O4-C4 bonds *are* defined in the patch # - the HO4-O4-C4 angle *is* defined in the patch # - the HO4-O4-C4-C3 (chi4 dihedral) is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the exclusions of HO4 and O4 *are* defined in the patch (replace those defined in the residue, which are identical) # - the exclusions of C4 are *not* defined in the patch (but in the residue) # # -- new atoms -- # (their exclusions replace those defined in the residue concerning preceding atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # excluded: O4 and C4 1 HO4 21 1 0.41000 0 2 2 3 # excluded: C4, C3 and C5 2 O4 3 16 -0.64200 0 3 3 4 13 # # -- replacement atoms -- # (exclusions defined in the residue) # 3 C4 14 3 0.23200 1 # # -- bonds -- # (new or replacement) # # NB 2 # IB JB MCB # HO4-O4 (new) 1 2 1 # C4-O4 (new) 2 3 20 # # -- bond angles -- # (new or replacement) # # NBA 1 # IB JB KB MCB # HO4-O4-C4 (new) 1 2 3 12 # # -- improper dihedrals -- # (new or replacement) # # NIDA 0 # IB JB KB LB MCB # # -- dihedrals -- # (new or replacement) # # NDA 0 # IB JB KB LB MCB # PHH, May 2011: the HO4-O4-C4-C3 dihedral was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue #@FREELINE END MTBUILDBLEND #@BLOCKTYPE _carbo INI RESID HEXP(-:6) # building block (residue, nucleotide, etc.) # RNME C6OH # # initial HO6-O6-C6- group for carbohydrates, to be used with a @*6 residue # # number of atoms, number of atoms to be replaced # NMAT NREP 3 1 # # - the HO6-O6 and O6-C6 bonds *are* defined in the patch # - the HO6-O6-C6 angle *is* defined in the patch # - the HO6-O6-C6-C5 (chi6 dihedral) is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the exclusions of HO6 and O6 *are* defined in the patch (replace those defined in the residue, which are identical) # - the exclusions of C6 are *not* defined in the patch (but in the residue) # # -- new atoms -- # (their exclusions replace those defined in the residue concerning preceding atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # excluded: O6 and C6 1 HO6 21 1 0.41000 0 2 2 3 # excluded: C6 and C5 2 O6 3 16 -0.64200 0 2 3 13 # # -- replacement atoms -- # (exclusions defined in the residue) # 3 C6 15 4 0.23200 1 # # -- bonds -- # (new or replacement) # # NB 2 # IB JB MCB # HO6-O6 (new) 1 2 1 # C6-O6 (new) 2 3 20 # # -- bond angles -- # (new or replacement) # # NBA 1 # IB JB KB MCB # HO6-O6-C6 (new) 1 2 3 12 # # -- improper dihedrals -- # (new or replacement) # # NIDA 0 # IB JB KB LB MCB # # -- dihedrals -- # (new or replacement) # # NDA 0 # IB JB KB LB MCB # PHH, May 2011: the HO6-O6-C6-C5 dihedral was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue #@FREELINE END