TITLE File : 53a6@OXY_small.mtb Force field : 53A6@OXY (condensed-phase simulations) Reference : Horta et al. J. Chem. Theory Comput. 2011, 7, 1016-1031 File content : molecular topology building blocks (small organic molecules) Format : GROMOS11 Initial file : PHH, BACH, Zuerich, Dec. 2010 Time stamp : PHH, Thu Nov 10 22:13:29 CET 2011 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 : ***warning*** 53A(B)6_OXY is not a slight variant of 53A(B)6, it is really a different force field (intermediate step to a new version, tentatively 61A8, to be released soon) Remark : Change from 53A(B)6 involves different Lennard-Jones parameters for the atom types O, OA and OE, and different charges for the oxygen-containing chemical functions Remark : Parameterization against pure-liquid and solvation (water, cyclohexane) properties of model oxygen-containing organic compounds Remark : information on the compound namings can be found just below the TITLE block Remark : versions beyond 54A(B)7 [including 53A(B)6@OXY and 56A(B)6@CARBO] are only available in GROMOS11 format (release of May 2011) 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, 09.11.2011: Renamed 53A6_OXY to 53A6@OXY (@: force-field variant; _: auxiliary mtb). PHH, 09.11.2011: Reintroduced a FORCEFIELD block in all GROMOS11 files. 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). END FORCEFIELD 53A6@OXY END # # Nomenclature of the building blocks: # ==================================== # # ALCOHOLS: # MTL - methanol # ETL - ethanol # 1PL - 1-propanol # 2PL - 2-propanol # BTL - 1-butanol # PTL - 1-pentanol # HXL - 1-hexanol # HPL - 1-heptanol # OTL - 1-octanol # 2BTL - 2-butanol # 2PTL - 2-pentanol # 3PTL - 3-pentanol # CHXL - cyclohexanol # 2M2P - 2-methyl-2-propanol # 2M2B - 2-methyl-2-butanol # ETHERS: # DME - dimethylether # DEE - diethylether # MPH - methylpropylether # DXE - 1,2-dimethoxiethane # ALDEHYDES: # EAL - ethanal # PAL - propanal # BAL - butanal # KETONES: # PPN - propanone # BTN - butanone # 2PN - 2-pentanone # 3PN - 3-pentanone # 2HN - 2-hexanone # 3HN - 3-hexanone # ESTERS: # EAE - ethylacetate # MPE - methylpropanoate # PAE - propylacetate # BAE - butylacetate # ACIDS: # ACA - acetic acid # PPA - propanoic acid # BTA - butanoic acid # OTHERS: # CHE - cyclohexane # PHYSICALCONSTANTS # 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 # SPDL: Speed of light (in nm/ps) 2.9979245800E05 # BOLTZ: Boltzmann's constant 8.31441E-03 END LINKEXCLUSIONS #nearest neighbour exclusions when linking #NRNE 2 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE MTL # building block (residue, nucleotide, etc.) # RNME MTL # number of atoms, number of preceding exclusions # NMAT NLIN 3 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H1 21 1 0.41000 0 2 2 3 2 O1 3 16 -0.70000 0 1 3 3 C1 16 5 0.29000 1 0 # bonds # NB 2 # IB JB MCB 1 2 1 2 3 18 # bond angles # NBA 1 # IB JB KB MCB 1 2 3 12 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE ETL # building block (residue, nucleotide, etc.) # RNME ETL # number of atoms, number of preceding exclusions # NMAT NLIN 4 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H1 21 1 0.41000 0 2 2 3 2 O1 3 16 -0.70000 0 2 3 4 3 C1 15 4 0.29000 1 1 4 4 C2 16 5 0.00000 1 0 # bonds # NB 3 # IB JB MCB 1 2 1 2 3 18 3 4 27 # bond angles # NBA 2 # IB JB KB MCB 1 2 3 12 2 3 4 15 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 1 2 3 4 23 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE 1PL # building block (residue, nucleotide, etc.) # RNME 1PL # number of atoms, number of preceding exclusions # NMAT NLIN 5 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H1 21 1 0.41000 0 2 2 3 2 O1 3 16 -0.70000 0 2 3 4 3 C1 15 4 0.29000 1 2 4 5 4 C2 15 4 0.00000 0 1 5 5 C3 16 5 0.00000 1 0 # bonds # NB 4 # IB JB MCB 1 2 1 2 3 18 3 4 27 4 5 27 # bond angles # NBA 3 # IB JB KB MCB 1 2 3 12 2 3 4 15 3 4 5 15 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 2 # IB JB KB LB MCB 1 2 3 4 23 2 3 4 5 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE 2PL # building block (residue, nucleotide, etc.) # RNME 2PL # number of atoms, number of preceding exclusions # NMAT NLIN 5 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 16 5 0.00000 1 3 2 4 5 2 O1 3 16 -0.70000 0 3 3 4 5 3 H1 21 1 0.41000 0 1 4 4 C2 14 3 0.29000 1 1 5 5 C3 16 5 0.00000 1 0 # bonds # NB 4 # IB JB MCB 1 4 27 2 3 1 2 4 18 4 5 27 # bond angles # NBA 4 # IB JB KB MCB 3 2 4 12 1 4 2 15 1 4 5 15 2 4 5 15 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 4 1 2 5 2 # dihedrals # NDA 1 # IB JB KB LB MCB 3 2 4 1 23 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE BTL # building block (residue, nucleotide, etc.) # RNME BTL # number of atoms, number of preceding exclusions # NMAT NLIN 6 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H1 21 1 0.41000 0 2 2 3 2 O1 3 16 -0.70000 0 2 3 4 3 C1 15 4 0.29000 1 2 4 5 4 C2 15 4 0.00000 0 2 5 6 5 C3 15 4 0.00000 0 1 6 6 C4 16 5 0.00000 1 0 # bonds # NB 5 # IB JB MCB 1 2 1 2 3 18 3 4 27 4 5 27 5 6 27 # bond angles # NBA 4 # IB JB KB MCB 1 2 3 12 2 3 4 15 3 4 5 15 4 5 6 15 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 3 # IB JB KB LB MCB 1 2 3 4 23 2 3 4 5 34 3 4 5 6 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE PTL # building block (residue, nucleotide, etc.) # RNME PTL # number of atoms, number of preceding exclusions # NMAT NLIN 7 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H1 21 1 0.41000 0 2 2 3 2 O1 3 16 -0.70000 0 2 3 4 3 C1 15 4 0.29000 1 2 4 5 4 C2 15 4 0.00000 0 2 5 6 5 C3 15 4 0.00000 1 2 6 7 6 C4 15 4 0.00000 0 1 7 7 C5 16 5 0.00000 1 0 # bonds # NB 6 # IB JB MCB 1 2 1 2 3 18 3 4 27 4 5 27 5 6 27 6 7 27 # bond angles # NBA 5 # IB JB KB MCB 1 2 3 12 2 3 4 15 3 4 5 15 4 5 6 15 5 6 7 15 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 4 # IB JB KB LB MCB 1 2 3 4 23 2 3 4 5 34 3 4 5 6 34 4 5 6 7 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE HXL # building block (residue, nucleotide, etc.) # RNME HXL # number of atoms, number of preceding exclusions # NMAT NLIN 8 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H1 21 1 0.41000 0 2 2 3 2 O1 3 16 -0.70000 0 2 3 4 3 C1 15 4 0.29000 1 2 4 5 4 C2 15 4 0.00000 0 2 5 6 5 C3 15 4 0.00000 0 2 6 7 6 C4 15 4 0.00000 1 2 7 8 7 C5 15 4 0.00000 0 1 8 8 C6 16 5 0.00000 1 0 # bonds # NB 7 # IB JB MCB 1 2 1 2 3 18 3 4 27 4 5 27 5 6 27 6 7 27 7 8 27 # bond angles # NBA 6 # IB JB KB MCB 1 2 3 12 2 3 4 15 3 4 5 15 4 5 6 15 5 6 7 15 6 7 8 15 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 5 # IB JB KB LB MCB 1 2 3 4 23 2 3 4 5 34 3 4 5 6 34 4 5 6 7 34 5 6 7 8 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE HPL # building block (residue, nucleotide, etc.) # RNME HPL # number of atoms, number of preceding exclusions # NMAT NLIN 9 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H1 21 1 0.41000 0 2 2 3 2 O1 3 16 -0.70000 0 2 3 4 3 C1 15 4 0.29000 1 2 4 5 4 C2 15 4 0.00000 0 2 5 6 5 C3 15 4 0.00000 1 2 6 7 6 C4 15 4 0.00000 0 2 7 8 7 C5 15 4 0.00000 1 2 8 9 8 C6 15 4 0.00000 0 1 9 9 C7 16 5 0.00000 1 0 # bonds # NB 8 # IB JB MCB 1 2 1 2 3 18 3 4 27 4 5 27 5 6 27 6 7 27 7 8 27 8 9 27 # bond angles # NBA 7 # IB JB KB MCB 1 2 3 12 2 3 4 15 3 4 5 15 4 5 6 15 5 6 7 15 6 7 8 15 7 8 9 15 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 6 # IB JB KB LB MCB 1 2 3 4 23 2 3 4 5 34 3 4 5 6 34 4 5 6 7 34 5 6 7 8 34 6 7 8 9 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE OTL # building block (residue, nucleotide, etc.) # RNME OTL # number of atoms, number of preceding exclusions # NMAT NLIN 10 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H1 21 1 0.41000 0 2 2 3 2 O1 3 16 -0.70000 0 2 3 4 3 C1 15 4 0.29000 1 2 4 5 4 C2 15 4 0.00000 0 2 5 6 5 C3 15 4 0.00000 0 2 6 7 6 C4 15 4 0.00000 1 2 7 8 7 C5 15 4 0.00000 0 2 8 9 8 C6 15 4 0.00000 1 2 9 10 9 C7 15 4 0.00000 0 1 10 10 C8 16 5 0.00000 1 0 # bonds # NB 9 # IB JB MCB 1 2 1 2 3 18 3 4 27 4 5 27 5 6 27 6 7 27 7 8 27 8 9 27 9 10 27 # bond angles # NBA 8 # IB JB KB MCB 1 2 3 12 2 3 4 15 3 4 5 15 4 5 6 15 5 6 7 15 6 7 8 15 7 8 9 15 8 9 10 15 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 7 # IB JB KB LB MCB 1 2 3 4 23 2 3 4 5 34 3 4 5 6 34 4 5 6 7 34 5 6 7 8 34 6 7 8 9 34 7 8 9 10 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE 2BTL # building block (residue, nucleotide, etc.) # RNME 2BTL # number of atoms, number of preceding exclusions # NMAT NLIN 6 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 16 5 0.00000 1 3 2 3 5 2 C2 14 3 0.29000 0 4 3 4 5 6 3 O1 3 16 -0.70000 0 2 4 5 4 H1 21 1 0.41000 1 0 5 C3 15 4 0.00000 0 1 6 6 C4 16 5 0.00000 1 0 # bonds # NB 5 # IB JB MCB 1 2 27 2 3 18 2 5 27 3 4 1 5 6 27 # bond angles # NBA 5 # IB JB KB MCB 1 2 3 15 1 2 5 15 3 2 5 15 2 3 4 12 2 5 6 15 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 2 1 3 5 2 # dihedrals # NDA 2 # IB JB KB LB MCB 1 2 3 4 23 1 2 5 6 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE 2PTL # building block (residue, nucleotide, etc.) # RNME 2PTL # number of atoms, number of preceding exclusions # NMAT NLIN 7 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 16 5 0.00000 1 3 2 3 5 2 C2 14 3 0.29000 0 4 3 4 5 6 3 O1 3 16 -0.70000 0 2 4 5 4 H1 21 1 0.41000 1 0 5 C3 15 4 0.00000 0 2 6 7 6 C4 15 4 0.00000 0 1 7 7 C5 16 5 0.00000 1 0 # bonds # NB 6 # IB JB MCB 1 2 27 2 3 18 2 5 27 3 4 1 5 6 27 6 7 27 # bond angles # NBA 6 # IB JB KB MCB 1 2 3 15 1 2 5 15 3 2 5 15 2 3 4 12 2 5 6 15 5 6 7 15 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 2 1 3 5 2 # dihedrals # NDA 3 # IB JB KB LB MCB 1 2 3 4 23 1 2 5 6 34 2 5 6 7 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE 3PTL # building block (residue, nucleotide, etc.) # RNME 3PTL # number of atoms, number of preceding exclusions # NMAT NLIN 7 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 16 5 0.00000 0 2 2 3 2 C2 15 4 0.00000 1 3 3 4 6 3 C3 14 3 0.29000 0 4 4 5 6 7 4 O1 3 16 -0.70000 0 2 5 6 5 H1 21 1 0.41000 1 0 6 C4 15 4 0.00000 0 1 7 7 C5 16 5 0.00000 1 0 # bonds # NB 6 # IB JB MCB 1 2 27 2 3 27 3 4 18 3 6 27 4 5 1 6 7 27 # bond angles # NBA 6 # IB JB KB MCB 1 2 3 15 2 3 4 15 2 3 6 15 4 3 6 15 3 4 5 12 3 6 7 15 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 6 2 4 3 2 # dihedrals # NDA 3 # IB JB KB LB MCB 1 2 3 4 34 2 3 4 5 23 2 3 6 7 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE CHXL # building block (residue, nucleotide, etc.) # RNME CHXL # number of atoms, number of preceding exclusions # NMAT NLIN 8 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 14 3 0.29000 0 6 2 3 4 5 7 8 2 O1 3 16 -0.70000 0 3 3 4 8 3 H1 21 1 0.41000 1 0 4 C2 18 4 0.00000 0 3 5 6 8 5 C3 18 4 0.00000 1 2 6 7 6 C4 18 4 0.00000 1 2 7 8 7 C5 18 4 0.00000 0 1 8 8 C6 18 4 0.00000 1 0 # bonds # NB 8 # IB JB MCB 1 2 18 1 4 27 1 8 27 2 3 1 4 5 27 5 6 27 6 7 27 7 8 27 # bond angles # NBA 9 # IB JB KB MCB 2 1 4 15 2 1 8 15 4 1 8 8 1 2 3 12 1 4 5 8 4 5 6 8 5 6 7 8 6 7 8 8 1 8 7 8 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 8 2 4 1 2 # dihedrals # NDA 7 # IB JB KB LB MCB 4 1 2 3 23 2 1 4 5 34 2 1 8 7 34 1 4 5 6 34 4 5 6 7 34 5 6 7 8 34 6 7 8 1 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE 2M2P # building block (residue, nucleotide, etc.) # RNME 2M2P # number of atoms, number of preceding exclusions # NMAT NLIN 6 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 13 12 0.29000 0 5 2 3 4 5 6 2 O1 3 16 -0.70000 0 4 3 4 5 6 3 H1 21 1 0.41000 1 0 4 C2 16 5 0.00000 1 2 5 6 5 C3 16 5 0.00000 1 1 6 6 C4 16 5 0.00000 1 0 # bonds # NB 5 # IB JB MCB 1 2 18 1 4 27 1 5 27 1 6 27 2 3 1 # bond angles # NBA 7 # IB JB KB MCB 2 1 4 15 2 1 5 15 2 1 6 15 4 1 5 15 4 1 6 15 5 1 6 15 1 2 3 12 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 4 1 2 3 23 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE 2M2B # building block (residue, nucleotide, etc.) # RNME 2M2B # number of atoms, number of preceding exclusions # NMAT NLIN 7 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 13 12 0.29000 0 6 2 3 4 5 6 7 2 O1 3 16 -0.70000 0 4 3 4 5 6 3 H1 21 1 0.41000 1 0 4 C2 16 5 0.00000 1 2 5 6 5 C3 16 5 0.00000 1 1 6 6 C4 15 4 0.00000 0 1 7 7 C5 16 5 0.00000 1 0 # bonds # NB 6 # IB JB MCB 1 2 18 1 4 27 1 5 27 1 6 27 2 3 1 6 7 27 # bond angles # NBA 8 # IB JB KB MCB 2 1 4 15 2 1 5 15 2 1 6 15 4 1 5 15 4 1 6 15 5 1 6 15 1 2 3 12 1 6 7 15 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 2 # IB JB KB LB MCB 4 1 2 3 23 2 1 6 7 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE DME # building block (residue, nucleotide, etc.) # RNME DME # number of atoms, number of preceding exclusions # NMAT NLIN 3 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C2 16 5 0.29000 0 2 2 3 2 O1 4 16 -0.58000 0 1 3 3 C3 16 5 0.29000 1 0 # bonds # NB 2 # IB JB MCB 1 2 18 2 3 18 # bond angles # NBA 1 # IB JB KB MCB 1 2 3 15 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE DEE # building block (residue, nucleotide, etc.) # RNME DEE # number of atoms, number of preceding exclusions # NMAT NLIN 5 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 16 5 0.00000 1 2 2 3 2 C2 15 4 0.29000 0 2 3 4 3 O1 4 16 -0.58000 0 2 4 5 4 C3 15 4 0.29000 1 1 5 5 C4 16 5 0.00000 1 0 # bonds # NB 4 # IB JB MCB 1 2 27 2 3 18 3 4 18 4 5 27 # bond angles # NBA 3 # IB JB KB MCB 1 2 3 15 2 3 4 15 3 4 5 15 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 2 # IB JB KB LB MCB 1 2 3 4 23 2 3 4 5 23 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE MPH # building block (residue, nucleotide, etc.) # RNME MPH # number of atoms, number of preceding exclusions # NMAT NLIN 5 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 16 5 0.29000 0 2 2 3 2 O1 4 16 -0.58000 0 2 3 4 3 C2 15 4 0.29000 1 2 4 5 4 C3 15 4 0.00000 0 1 5 5 C4 16 5 0.00000 1 0 # bonds # NB 4 # IB JB MCB 1 2 18 2 3 18 3 4 27 4 5 27 # bond angles # NBA 3 # IB JB KB MCB 1 2 3 15 2 3 4 15 3 4 5 15 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 2 # IB JB KB LB MCB 1 2 3 4 23 2 3 4 5 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE DXE # building block (residue, nucleotide, etc.) # RNME DXE # number of atoms, number of preceding exclusions # NMAT NLIN 6 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 16 5 0.29000 0 2 2 3 2 O1 4 16 -0.58000 0 2 3 4 3 C2 15 4 0.29000 1 2 4 5 4 C3 15 4 0.29000 0 2 5 6 5 O2 4 16 -0.58000 0 1 6 6 C4 16 5 0.29000 1 0 # bonds # NB 5 # IB JB MCB 1 2 18 2 3 18 3 4 27 4 5 18 5 6 18 # bond angles # NBA 4 # IB JB KB MCB 1 2 3 15 2 3 4 15 3 4 5 15 4 5 6 15 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 3 # IB JB KB LB MCB 1 2 3 4 23 2 3 4 5 34 3 4 5 6 23 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE EAL # building block (residue, nucleotide, etc.) # RNME EAL # number of atoms, number of preceding exclusions # NMAT NLIN 4 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 12 12 0.37500 0 3 2 3 4 2 O1 1 16 -0.47500 0 2 3 4 3 H1 20 1 0.10000 0 1 4 4 C2 16 5 0.00000 1 0 # bonds # NB 3 # IB JB MCB 1 2 5 1 3 3 1 4 27 # bond angles # NBA 3 # IB JB KB MCB 2 1 3 25 2 1 4 33 3 1 4 21 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 1 2 3 4 1 # dihedrals # NDA 0 # IB JB KB LB MCB # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE PAL # building block (residue, nucleotide, etc.) # RNME PAL # number of atoms, number of preceding exclusions # NMAT NLIN 5 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 12 12 0.37500 0 4 2 3 4 5 2 O1 1 16 -0.47500 0 2 3 4 3 H1 20 1 0.10000 1 1 4 4 C2 15 4 0.00000 0 1 5 5 C3 16 5 0.00000 1 0 # bonds # NB 4 # IB JB MCB 1 2 5 1 3 3 1 4 27 4 5 27 # bond angles # NBA 4 # IB JB KB MCB 2 1 3 25 2 1 4 33 3 1 4 21 1 4 5 15 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 1 2 3 4 1 # dihedrals # NDA 1 # IB JB KB LB MCB 2 1 4 5 40 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE BAL # building block (residue, nucleotide, etc.) # RNME BAL # number of atoms, number of preceding exclusions # NMAT NLIN 6 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 12 12 0.37500 0 4 2 3 4 5 2 O1 1 16 -0.47500 0 2 3 4 3 H1 20 1 0.10000 1 1 4 4 C2 15 4 0.00000 0 2 5 6 5 C3 15 4 0.00000 0 1 6 6 C4 16 5 0.00000 1 0 # bonds # NB 5 # IB JB MCB 1 2 5 1 3 3 1 4 27 4 5 27 5 6 27 # bond angles # NBA 5 # IB JB KB MCB 2 1 3 25 2 1 4 33 3 1 4 21 1 4 5 15 4 5 6 15 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 1 2 3 4 1 # dihedrals # NDA 2 # IB JB KB LB MCB 2 1 4 5 40 1 4 5 6 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE PPN # building block (residue, nucleotide, etc.) # RNME PPN # number of atoms, number of preceding exclusions # NMAT NLIN 4 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 16 5 0.00000 1 3 2 3 4 2 C2 12 12 0.54000 0 2 3 4 3 O1 1 16 -0.54000 1 1 4 4 C3 16 5 0.00000 1 0 # bonds # NB 3 # IB JB MCB 1 2 27 2 3 5 2 4 27 # bond angles # NBA 3 # IB JB KB MCB 1 2 3 31 1 2 4 21 3 2 4 31 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 2 1 3 4 1 # dihedrals # NDA 0 # IB JB KB LB MCB # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE BTN # building block (residue, nucleotide, etc.) # RNME BTN # number of atoms, number of preceding exclusions # NMAT NLIN 5 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 16 5 0.00000 1 3 2 3 4 2 C2 12 12 0.54000 0 3 3 4 5 3 O1 1 16 -0.54000 1 1 4 4 C3 15 4 0.00000 0 1 5 5 C4 16 5 0.00000 1 0 # bonds # NB 4 # IB JB MCB 1 2 27 2 3 5 2 4 27 4 5 27 # bond angles # NBA 4 # IB JB KB MCB 1 2 3 31 1 2 4 21 3 2 4 31 2 4 5 15 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 2 1 3 4 1 # dihedrals # NDA 1 # IB JB KB LB MCB 1 2 4 5 40 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE 2PN # building block (residue, nucleotide, etc.) # RNME 2PN # number of atoms, number of preceding exclusions # NMAT NLIN 6 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 16 5 0.00000 1 3 2 3 4 2 C2 12 12 0.54000 0 3 3 4 5 3 O1 1 16 -0.54000 1 1 4 4 C3 15 4 0.00000 0 2 5 6 5 C4 15 4 0.00000 0 1 6 6 C5 16 5 0.00000 1 0 # bonds # NB 5 # IB JB MCB 1 2 27 2 3 5 2 4 27 4 5 27 5 6 27 # bond angles # NBA 5 # IB JB KB MCB 1 2 3 31 1 2 4 21 3 2 4 31 2 4 5 15 4 5 6 15 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 2 1 3 4 1 # dihedrals # NDA 2 # IB JB KB LB MCB 1 2 4 5 40 2 4 5 6 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE 3PN # building block (residue, nucleotide, etc.) # RNME 3PN # number of atoms, number of preceding exclusions # NMAT NLIN 6 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 16 5 0.00000 0 2 2 3 2 C2 15 4 0.00000 1 3 3 4 5 3 C3 12 12 0.54000 0 3 4 5 6 4 O1 1 16 -0.54000 1 1 5 5 C4 15 4 0.00000 0 1 6 6 C5 16 5 0.00000 1 0 # bonds # NB 5 # IB JB MCB 1 2 27 2 3 27 3 4 5 3 5 27 5 6 27 # bond angles # NBA 5 # IB JB KB MCB 1 2 3 15 2 3 4 31 2 3 5 21 4 3 5 31 3 5 6 15 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 3 2 4 5 1 # dihedrals # NDA 2 # IB JB KB LB MCB 1 2 3 4 40 2 3 5 6 40 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE 2HN # building block (residue, nucleotide, etc.) # RNME 2HN # number of atoms, number of preceding exclusions # NMAT NLIN 7 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 16 5 0.00000 1 3 2 3 4 2 C2 12 12 0.54000 0 3 3 4 5 3 O1 1 16 -0.54000 1 1 4 4 C3 15 4 0.00000 0 2 5 6 5 C4 15 4 0.00000 1 2 6 7 6 C5 15 4 0.00000 0 1 7 7 C6 16 5 0.00000 1 0 # bonds # NB 6 # IB JB MCB 1 2 27 2 3 5 2 4 27 4 5 27 5 6 27 6 7 27 # bond angles # NBA 6 # IB JB KB MCB 1 2 3 31 1 2 4 21 3 2 4 31 2 4 5 15 4 5 6 15 5 6 7 15 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 2 1 3 4 1 # dihedrals # NDA 3 # IB JB KB LB MCB 1 2 4 5 40 2 4 5 6 34 4 5 6 7 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE 3HN # building block (residue, nucleotide, etc.) # RNME 3HN # number of atoms, number of preceding exclusions # NMAT NLIN 7 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 16 5 0.00000 0 2 2 3 2 C2 15 4 0.00000 1 3 3 4 5 3 C3 12 12 0.54000 0 3 4 5 6 4 O1 1 16 -0.54000 1 1 5 5 C4 15 4 0.00000 0 2 6 7 6 C5 15 4 0.00000 0 1 7 7 C6 16 5 0.00000 1 0 # bonds # NB 6 # IB JB MCB 1 2 27 2 3 27 3 4 5 3 5 27 5 6 27 6 7 27 # bond angles # NBA 6 # IB JB KB MCB 1 2 3 15 2 3 4 31 2 3 5 21 4 3 5 31 3 5 6 15 5 6 7 15 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 3 2 4 5 1 # dihedrals # NDA 3 # IB JB KB LB MCB 1 2 3 4 40 2 3 5 6 40 3 5 6 7 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE ACA # building block (residue, nucleotide, etc.) # RNME ACA # number of atoms, number of preceding exclusions # NMAT NLIN 5 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 16 5 0.00000 1 3 2 3 4 2 C2 12 12 0.55000 0 3 3 4 5 3 O1 1 16 -0.55000 1 1 4 4 O2 3 16 -0.41000 0 1 5 5 H1 21 1 0.41000 1 0 # bonds # NB 4 # IB JB MCB 1 2 27 2 3 5 2 4 13 4 5 1 # bond angles # NBA 4 # IB JB KB MCB 1 2 3 35 1 2 4 16 3 2 4 31 2 4 5 12 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 2 1 3 4 1 # dihedrals # NDA 1 # IB JB KB LB MCB 1 2 4 5 12 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE PPA # building block (residue, nucleotide, etc.) # RNME PPA # number of atoms, number of preceding exclusions # NMAT NLIN 6 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 12 12 0.55000 0 5 2 3 4 5 6 2 O1 1 16 -0.55000 1 2 3 5 3 O2 3 16 -0.41000 0 2 4 5 4 H1 21 1 0.41000 1 0 5 C2 15 4 0.00000 0 1 6 6 C3 16 5 0.00000 1 0 # bonds # NB 5 # IB JB MCB 1 2 5 1 3 13 1 5 27 3 4 1 5 6 27 # bond angles # NBA 5 # IB JB KB MCB 2 1 3 31 2 1 5 35 3 1 5 16 1 3 4 12 1 5 6 15 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 1 2 3 5 1 # dihedrals # NDA 2 # IB JB KB LB MCB 2 1 3 4 12 2 1 5 6 40 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE BTA # building block (residue, nucleotide, etc.) # RNME BTA # number of atoms, number of preceding exclusions # NMAT NLIN 7 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 12 12 0.55000 0 5 2 3 4 5 6 2 O1 1 16 -0.55000 1 2 3 5 3 O2 3 16 -0.41000 0 2 4 5 4 H1 21 1 0.41000 1 0 5 C2 15 4 0.00000 0 2 6 7 6 C3 15 4 0.00000 0 1 7 7 C4 16 5 0.00000 1 0 # bonds # NB 6 # IB JB MCB 1 2 5 1 3 13 1 5 27 3 4 1 5 6 27 6 7 27 # bond angles # NBA 6 # IB JB KB MCB 2 1 3 31 2 1 5 35 3 1 5 16 1 3 4 12 1 5 6 15 5 6 7 15 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 1 2 3 5 1 # dihedrals # NDA 3 # IB JB KB LB MCB 2 1 3 4 12 2 1 5 6 40 1 5 6 7 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE EAE # building block (residue, nucleotide, etc.) # RNME EAE # number of atoms, number of preceding exclusions # NMAT NLIN 6 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 16 5 0.00000 1 3 2 3 4 2 O1 1 16 -0.55000 0 2 3 4 3 O2 4 16 -0.37000 0 3 4 5 6 4 C2 12 12 0.63000 0 1 5 5 C3 15 4 0.29000 1 1 6 6 C4 16 5 0.00000 1 0 # bonds # NB 5 # IB JB MCB 1 4 27 2 4 5 3 4 13 3 5 18 5 6 27 # bond angles # NBA 5 # IB JB KB MCB 4 3 5 22 1 4 2 35 1 4 3 16 2 4 3 31 3 5 6 15 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 4 1 2 3 1 # dihedrals # NDA 2 # IB JB KB LB MCB 5 3 4 1 12 4 3 5 6 29 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE MPE # building block (residue, nucleotide, etc.) # RNME MPE # Methylpropanoate # number of atoms, number of preceding exclusions # NMAT NLIN 6 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 16 5 0.29000 0 2 2 3 2 O11 4 16 -0.37000 0 3 3 4 5 3 C11 12 12 0.63000 0 3 4 5 6 4 O12 1 16 -0.55000 1 1 5 5 C12 15 4 0.00000 1 1 6 6 C13 16 5 0.00000 1 0 # bonds # NB 5 # IB JB MCB 1 2 18 2 3 13 3 4 5 3 5 27 5 6 27 # bond angles # NBA 5 # IB JB KB MCB 1 2 3 22 2 3 4 31 2 3 5 16 4 3 5 35 3 5 6 15 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 3 2 5 4 1 # dihedrals # NDA 2 # IB JB KB LB MCB 1 2 3 5 12 2 3 5 6 40 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE PAE # building block (residue, nucleotide, etc.) # RNME PAE # number of atoms, number of preceding exclusions # NMAT NLIN 7 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C12 16 5 0.00000 1 3 2 3 4 2 C11 12 12 0.63000 0 3 3 4 5 3 O12 1 16 -0.55000 0 1 4 4 O11 4 16 -0.37000 0 2 5 6 5 C1 15 4 0.29000 1 2 6 7 6 C2 15 4 0.00000 0 1 7 7 C3 16 5 0.00000 1 0 # bonds # NB 6 # IB JB MCB 1 2 27 2 3 5 2 4 13 4 5 18 5 6 27 6 7 27 # bond angles # NBA 6 # IB JB KB MCB 1 2 3 35 1 2 4 16 3 2 4 31 2 4 5 22 4 5 6 15 5 6 7 15 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 2 1 3 4 1 # dihedrals # NDA 3 # IB JB KB LB MCB 1 2 4 5 12 2 4 5 6 29 4 5 6 7 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE BAE # building block (residue, nucleotide, etc.) # RNME BAE # number of atoms, number of preceding exclusions # NMAT NLIN 8 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C12 16 5 0.00000 1 3 2 3 4 2 C11 12 12 0.63000 0 3 3 4 5 3 O12 1 16 -0.55000 0 1 4 4 O11 4 16 -0.37000 0 2 5 6 5 C1 15 4 0.29000 1 2 6 7 6 C2 15 4 0.00000 0 2 7 8 7 C3 15 4 0.00000 0 1 8 8 C4 16 5 0.00000 1 0 # bonds # NB 7 # IB JB MCB 1 2 27 2 3 5 2 4 13 4 5 18 5 6 27 6 7 27 7 8 27 # bond angles # NBA 7 # IB JB KB MCB 1 2 3 35 1 2 4 16 3 2 4 31 2 4 5 22 4 5 6 15 5 6 7 15 6 7 8 15 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 2 1 3 4 1 # dihedrals # NDA 4 # IB JB KB LB MCB 1 2 4 5 12 2 4 5 6 29 4 5 6 7 34 5 6 7 8 34 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 53a6@OXY_small.mtb SOL TYPE CHE # building block (residue, nucleotide, etc.) # RNME CHE # number of atoms, number of preceding exclusions # NMAT NLIN 6 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 18 4 0.00000 0 4 2 3 5 6 2 C2 18 4 0.00000 1 3 3 4 6 3 C3 18 4 0.00000 0 2 4 5 4 C4 18 4 0.00000 1 2 5 6 5 C5 18 4 0.00000 0 1 6 6 C6 18 4 0.00000 1 0 # bonds # NB 6 # IB JB MCB 1 2 27 1 6 27 2 3 27 3 4 27 4 5 27 5 6 27 # bond angles # NBA 6 # IB JB KB MCB 1 2 3 8 2 3 4 8 3 4 5 8 4 5 6 8 1 6 5 8 2 1 6 8 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 6 # IB JB KB LB MCB 1 2 3 4 34 2 3 4 5 34 3 4 5 6 34 4 5 6 1 34 2 1 6 5 34 6 1 2 3 34 # LJ exceptions # NEX 0 #@FREELINE END