TITLE File : 54a8.mtb Force field : 54A8 (condensed-phase simulations) Reference : Reif et al. J. Chem. Theory Comput. 2012, in press File content : Molecular topology building blocks (alpha amino acids, nucleic acids, lipids) Format : GROMOS11 Initial file : MMR, PHH, CO Vienna/Zuerich, June 2012 Time stamp : PHH, Tue Jun 12 18:09:07 CEST 2012 Remark : ******************************************************************************** **** topologies must be built using a make_top version of June 2012 or later *** ******************************************************************************** Reason: make_top must recognize negative IAC in patches, which indicate the closest preceding atom with the indicated atom name (used in COO- and BOO- patches to locate the preceding CA) Remark : Change from 54A(B)7 involves a reparametrization of the charged amino-acid sidechains, of the charged peptide termini, of DPPC, and of uronate residues Remark : This file only differs from the 54A7 in the charged residues, in the charged terminal patches, and for DPPC (for the latter, the Chiu charges are still used, but there are changes in the CH3p parameters and the selection matrix for OM-CH3p, see ifp file) Remark : Note that the COO- patch is special (overall neutral pair of two non-neutral charge groups for CA and COO-; these could not be assembled in a single neutral charge group because the atoms are not consecutive) Remark : There is no B force-field version for this set (use 54B7 instead) 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, June 2012 - finalized for distribution on www.gromos.net Modifications : [list below changes after June 2012 - with initials, location and date - and update time stamp] END FORCEFIELD 54A8 END 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 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK ALA SOL TYPE APEP NAME Alanine # building block (residue, nucleotide, etc.) # RNME ALA # number of atoms, number of preceding exclusions # NMAT NLIN 6 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 5 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 4 4 5 6 7 4 CB 16 5 0.00000 1 1 5 # trailing atoms #ATOM ANM IACM MASS CGMICGM 5 C 12 12 0.45000 0 6 O 1 16 -0.45000 1 # bonds # NB 6 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 5 27 5 6 5 5 7 10 # bond angles # NBA 9 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 5 13 4 3 5 13 3 5 6 30 3 5 7 19 6 5 7 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 5 4 2 5 3 7 6 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 5 44 -1 1 3 5 43 1 3 5 7 45 1 3 5 7 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK ARG SOL TYPE APEP NAME Arginine (protonated; charge +e) # building block (residue, nucleotide, etc.) # RNME ARG # number of atoms, number of preceding exclusions # NMAT NLIN 17 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 16 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 16 17 18 4 CB 15 4 0.00000 0 3 5 6 16 5 CG 15 4 0.00000 1 2 6 7 6 CD 15 4 0.09000 0 3 7 8 9 # Change 54A7->54A8 --- new charges for atoms 7-15 7 NE 11 14 -0.10500 0 4 8 9 10 13 8 HE 21 1 0.34500 0 1 9 9 CZ 12 12 0.01000 0 6 10 11 12 13 14 15 10 NH1 10 14 -0.36000 0 3 11 12 13 11 HH11 21 1 0.34500 0 1 12 12 HH12 21 1 0.34500 0 0 13 NH2 10 14 -0.36000 0 2 14 15 14 HH21 21 1 0.34500 0 1 15 15 HH22 21 1 0.34500 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 16 C 12 12 0.45000 0 17 O 1 16 -0.45000 1 # bonds # NB 17 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 16 27 4 5 27 5 6 27 6 7 21 7 8 2 7 9 11 9 10 11 9 13 11 10 11 2 10 12 2 13 14 2 13 15 2 16 17 5 16 18 10 # bond angles # NBA 24 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 16 13 4 3 16 13 3 4 5 15 4 5 6 15 5 6 7 13 6 7 8 20 6 7 9 33 8 7 9 23 7 9 10 28 7 9 13 28 10 9 13 28 9 10 11 23 9 10 12 23 11 10 12 24 9 13 14 23 9 13 15 23 14 13 15 24 3 16 17 30 3 16 18 19 17 16 18 33 # improper dihedrals # NIDA 7 # IB JB KB LB MCB 1 -1 3 2 1 3 1 16 4 2 7 6 9 8 1 9 10 13 7 1 10 11 12 9 1 13 14 15 9 1 16 3 18 17 1 # dihedrals # NDA 12 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 16 44 -1 1 3 16 43 1 3 4 5 34 1 3 16 18 45 1 3 16 18 42 3 4 5 6 34 4 5 6 7 34 5 6 7 9 39 6 7 9 10 14 7 9 10 11 14 7 9 13 14 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK ARGN SOL TYPE APEP NAME Arginine (deprotonated; neutral) # building block (residue, nucleotide, etc.) # RNME ARGN # number of atoms, number of preceding exclusions # NMAT NLIN 16 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 15 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 15 16 17 4 CB 15 4 0.00000 1 3 5 6 15 5 CG 15 4 0.00000 0 2 6 7 6 CD 15 4 0.00000 1 3 7 8 9 7 NE 11 14 -0.31000 0 4 8 9 10 12 8 HE 21 1 0.31000 1 1 9 9 CZ 12 12 0.26600 0 5 10 11 12 13 14 10 NH1 11 14 -0.67400 0 2 11 12 11 HH1 21 1 0.40800 1 0 12 NH2 10 14 -0.88000 0 2 13 14 13 HH21 21 1 0.44000 0 1 14 14 HH22 21 1 0.44000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 15 C 12 12 0.45000 0 16 O 1 16 -0.45000 1 # bonds # NB 16 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 15 27 4 5 27 5 6 27 6 7 21 7 8 2 7 9 11 9 10 11 9 12 11 10 11 2 12 13 2 12 14 2 15 16 5 15 17 10 # bond angles # NBA 22 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 15 13 4 3 15 13 3 4 5 15 4 5 6 15 5 6 7 13 6 7 8 20 6 7 9 33 8 7 9 23 7 9 10 28 7 9 12 28 10 9 12 28 9 10 11 23 9 12 13 23 9 12 14 23 13 12 14 24 3 15 16 30 3 15 17 19 16 15 17 33 # improper dihedrals # NIDA 6 # IB JB KB LB MCB 1 -1 3 2 1 3 1 15 4 2 7 6 9 8 1 9 10 12 7 1 12 13 14 9 1 15 3 17 16 1 # dihedrals # NDA 12 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 15 44 -1 1 3 15 43 1 3 4 5 34 1 3 15 17 45 1 3 15 17 42 3 4 5 6 34 4 5 6 7 34 5 6 7 9 39 6 7 9 10 14 7 9 10 11 14 7 9 12 13 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK ASN SOL TYPE APEP NAME Asparagine # building block (residue, nucleotide, etc.) # RNME ASN # number of atoms, number of preceding exclusions # NMAT NLIN 11 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 10 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 10 11 12 4 CB 15 4 0.00000 1 4 5 6 7 10 5 CG 12 12 0.29000 0 4 6 7 8 9 6 OD1 1 16 -0.45000 0 1 7 7 ND2 7 14 -0.72000 0 2 8 9 8 HD21 21 1 0.44000 0 1 9 9 HD22 21 1 0.44000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 10 C 12 12 0.45000 0 11 O 1 16 -0.45000 1 # bonds # NB 11 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 10 27 4 5 27 5 6 5 5 7 9 7 8 2 7 9 2 10 11 5 10 12 10 # bond angles # NBA 16 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 10 13 4 3 10 13 3 4 5 15 4 5 6 30 4 5 7 19 6 5 7 33 5 7 8 23 5 7 9 23 8 7 9 24 3 10 11 30 3 10 12 19 11 10 12 33 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 1 -1 3 2 1 3 1 10 4 2 5 6 7 4 1 7 8 9 5 1 10 3 12 11 1 # dihedrals # NDA 8 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 10 44 -1 1 3 10 43 1 3 4 5 34 1 3 10 12 45 1 3 10 12 42 3 4 5 7 40 4 5 7 8 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK ASN1 SOL TYPE APEP NAME Asparagine (coordinated with ZN) # building block (residue, nucleotide, etc.) # RNME ASN1 # number of atoms, number of preceding exclusions # NMAT NLIN 11 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 10 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 10 11 12 4 CB 15 4 0.00000 1 4 5 6 7 10 5 CG 12 12 0.29000 0 4 6 7 8 9 6 OD1 1 16 -0.45000 0 1 7 7 ND2 8 14 -0.72000 0 2 8 9 8 HD21 21 1 0.44000 0 1 9 9 HD22 21 1 0.44000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 10 C 12 12 0.45000 0 11 O 1 16 -0.45000 1 # bonds # NB 11 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 10 27 4 5 27 5 6 5 5 7 9 7 8 2 7 9 2 10 11 5 10 12 10 # bond angles # NBA 16 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 10 13 4 3 10 13 3 4 5 15 4 5 6 30 4 5 7 19 6 5 7 33 5 7 8 23 5 7 9 23 8 7 9 24 3 10 11 30 3 10 12 19 11 10 12 33 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 1 -1 3 2 1 3 1 10 4 2 5 6 7 4 1 7 8 9 5 1 10 3 12 11 1 # dihedrals # NDA 8 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 10 44 -1 1 3 10 43 1 3 4 5 34 1 3 10 12 45 1 3 10 12 42 3 4 5 7 40 4 5 7 8 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK ASP SOL TYPE APEP NAME Aspartic acid (deprotonated; charge -e) # building block (residue, nucleotide, etc.) # RNME ASP # number of atoms, number of preceding exclusions # NMAT NLIN 9 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 # Change 54A7->54A8 --- new charges / altered CG definition for atoms 3-4 3 CA 14 3 0.00000 1 5 4 5 8 9 10 4 CB 15 4 0.16000 0 4 5 6 7 8 5 CG 12 12 0.27000 0 2 6 7 # Change 54A7->54A8 --- new charges for atoms 6-7 6 OD1 2 16 -0.71500 0 1 7 7 OD2 2 16 -0.71500 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 27 5 6 6 5 7 6 8 9 5 8 10 10 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 15 4 5 6 22 4 5 7 22 6 5 7 38 3 8 9 30 3 8 10 19 9 8 10 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 8 4 2 5 6 7 4 1 8 3 10 9 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 44 -1 1 3 8 43 1 3 4 5 34 1 3 8 10 45 1 3 8 10 42 3 4 5 6 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK ASPH SOL TYPE APEP NAME Aspartic acid (protonated; neutral) # building block (residue, nucleotide, etc.) # RNME ASPH # number of atoms, number of preceding exclusions # NMAT NLIN 10 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 9 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 9 10 11 4 CB 15 4 0.00000 1 4 5 6 7 9 5 CG 12 12 0.33000 0 3 6 7 8 6 OD1 1 16 -0.45000 0 1 7 7 OD2 3 16 -0.28800 0 1 8 8 HD2 21 1 0.40800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 9 C 12 12 0.45000 0 10 O 1 16 -0.45000 1 # bonds # NB 10 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 9 27 4 5 27 5 6 5 5 7 13 7 8 1 9 10 5 9 11 10 # bond angles # NBA 14 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 9 13 4 3 9 13 3 4 5 15 4 5 6 30 4 5 7 19 6 5 7 33 5 7 8 12 3 9 10 30 3 9 11 19 10 9 11 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 9 4 2 5 6 7 4 1 9 3 11 10 1 # dihedrals # NDA 8 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 9 44 -1 1 3 9 43 1 3 4 5 34 1 3 9 11 45 1 3 9 11 42 3 4 5 7 40 4 5 7 8 12 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK CYS SOL TYPE APEP NAME Cysteine (deprotonated; charge -0.5e) # building block (residue, nucleotide, etc.) # RNME CYS # number of atoms, number of preceding exclusions # NMAT NLIN 7 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 6 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 1 5 4 5 6 7 8 4 CB 15 4 -0.10000 0 2 5 6 5 SG 23 32 -0.40000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 12 12 0.45000 0 7 O 1 16 -0.45000 1 # bonds # NB 7 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 6 27 4 5 32 6 7 5 6 8 10 # bond angles # NBA 10 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 6 13 4 3 6 13 3 4 5 16 3 6 7 30 3 6 8 19 7 6 8 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 6 4 2 6 3 8 7 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 6 44 -1 1 3 6 43 1 3 4 5 34 1 3 6 8 45 1 3 6 8 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK CYSH SOL TYPE APEP NAME Cysteine (protonated; neutral) # building block (residue, nucleotide, etc.) # RNME CYSH # number of atoms, number of preceding exclusions # NMAT NLIN 8 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 7 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 1 5 4 5 7 8 9 4 CB 15 4 0.15000 0 3 5 6 7 5 SG 23 32 -0.37000 0 1 6 6 HG 21 1 0.22000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 7 C 12 12 0.45000 0 8 O 1 16 -0.45000 1 # bonds # NB 8 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 7 27 4 5 32 5 6 8 7 8 5 7 9 10 # bond angles # NBA 11 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 7 13 4 3 7 13 3 4 5 16 4 5 6 3 3 7 8 30 3 7 9 19 8 7 9 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 7 4 2 7 3 9 8 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 44 -1 1 3 7 43 1 3 4 5 34 1 3 7 9 45 1 3 7 9 42 3 4 5 6 26 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK CYS1 SOL TYPE APEP NAME Cysteine (1st member of S-S bridge) # building block (residue, nucleotide, etc.) # RNME CYS1 # number of atoms, number of preceding exclusions # NMAT NLIN 7 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 6 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 6 7 8 4 CB 15 4 0.00000 0 3 -5 5 6 5 SG 23 32 0.00000 1 2 -5 -4 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 12 12 0.45000 0 7 O 1 16 -0.45000 1 # bonds # NB 8 # IB JB MCB -5 5 36 1 2 2 1 3 21 3 4 27 3 6 27 4 5 32 6 7 5 6 8 10 # bond angles # NBA 12 # IB JB KB MCB -4 -5 5 6 -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 6 13 4 3 6 13 3 4 5 16 -5 5 4 6 3 6 7 30 3 6 8 19 7 6 8 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 6 4 2 6 3 8 7 1 # dihedrals # NDA 9 # IB JB KB LB MCB 5 -5 -4 -3 26 -4 -5 5 4 21 -2 -1 1 3 14 -1 1 3 6 44 -1 1 3 6 43 1 3 4 5 34 1 3 6 8 45 1 3 6 8 42 3 4 5 -5 26 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK CYS2 SOL TYPE APEP NAME Cysteine (2nd member of S-S bridge) # building block (residue, nucleotide, etc.) # RNME CYS2 # number of atoms, number of preceding exclusions # NMAT NLIN 7 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 6 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 6 7 8 4 CB 15 4 0.00000 0 2 5 6 5 SG 23 32 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 12 12 0.45000 0 7 O 1 16 -0.45000 1 # bonds # NB 7 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 6 27 4 5 32 6 7 5 6 8 10 # bond angles # NBA 10 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 6 13 4 3 6 13 3 4 5 16 3 6 7 30 3 6 8 19 7 6 8 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 6 4 2 6 3 8 7 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 6 44 -1 1 3 6 43 1 3 4 5 34 1 3 6 8 45 1 3 6 8 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK GLN SOL TYPE APEP NAME Glutamine # building block (residue, nucleotide, etc.) # RNME GLN # number of atoms, number of preceding exclusions # NMAT NLIN 12 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 11 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 11 12 13 4 CB 15 4 0.00000 0 3 5 6 11 5 CG 15 4 0.00000 1 3 6 7 8 6 CD 12 12 0.29000 0 4 7 8 9 10 7 OE1 1 16 -0.45000 0 1 8 8 NE2 7 14 -0.72000 0 2 9 10 9 HE21 21 1 0.44000 0 1 10 10 HE22 21 1 0.44000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 11 C 12 12 0.45000 0 12 O 1 16 -0.45000 1 # bonds # NB 12 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 11 27 4 5 27 5 6 27 6 7 5 6 8 9 8 9 2 8 10 2 11 12 5 11 13 10 # bond angles # NBA 17 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 11 13 4 3 11 13 3 4 5 15 4 5 6 15 5 6 7 30 5 6 8 19 7 6 8 33 6 8 9 23 6 8 10 23 9 8 10 24 3 11 12 30 3 11 13 19 12 11 13 33 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 1 -1 3 2 1 3 1 11 4 2 6 7 8 5 1 8 9 10 6 1 11 3 13 12 1 # dihedrals # NDA 9 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 11 44 -1 1 3 11 43 1 3 4 5 34 1 3 11 13 45 1 3 11 13 42 3 4 5 6 34 4 5 6 8 40 5 6 8 9 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK GLU SOL TYPE APEP NAME Glutamine acid (deprotonated; charge -e) # building block (residue, nucleotide, etc.) # RNME GLU # number of atoms, number of preceding exclusions # NMAT NLIN 10 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 9 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 9 10 11 # Change 54A7->54A8 --- new charges / altered CG definition for atoms 4-5 4 CB 15 4 0.00000 1 3 5 6 9 5 CG 15 4 0.16000 0 3 6 7 8 6 CD 12 12 0.27000 0 2 7 8 # Change 54A7->54A8 --- new charges for atoms 7-8 7 OE1 2 16 -0.71500 0 1 8 8 OE2 2 16 -0.71500 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 9 C 12 12 0.45000 0 10 O 1 16 -0.45000 1 # bonds # NB 10 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 9 27 4 5 27 5 6 27 6 7 6 6 8 6 9 10 5 9 11 10 # bond angles # NBA 14 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 9 13 4 3 9 13 3 4 5 15 4 5 6 15 5 6 7 22 5 6 8 22 7 6 8 38 3 9 10 30 3 9 11 19 10 9 11 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 9 4 2 6 7 8 5 1 9 3 11 10 1 # dihedrals # NDA 8 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 9 44 -1 1 3 9 43 1 3 4 5 34 1 3 9 11 45 1 3 9 11 42 3 4 5 6 34 4 5 6 8 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK GLUH SOL TYPE APEP NAME Glutamine acid (protonated; neutral) # building block (residue, nucleotide, etc.) # RNME GLUH # number of atoms, number of preceding exclusions # NMAT NLIN 11 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 10 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 10 11 12 4 CB 15 4 0.00000 0 3 5 6 10 5 CG 15 4 0.00000 1 3 6 7 8 6 CD 12 12 0.33000 0 3 7 8 9 7 OE1 1 16 -0.45000 0 1 8 8 OE2 3 16 -0.28800 0 1 9 9 HE2 21 1 0.40800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 10 C 12 12 0.45000 0 11 O 1 16 -0.45000 1 # bonds # NB 11 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 10 27 4 5 27 5 6 27 6 7 5 6 8 13 8 9 1 10 11 5 10 12 10 # bond angles # NBA 15 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 10 13 4 3 10 13 3 4 5 15 4 5 6 15 5 6 7 30 5 6 8 19 7 6 8 33 6 8 9 12 3 10 11 30 3 10 12 19 11 10 12 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 10 4 2 6 7 8 5 1 10 3 12 11 1 # dihedrals # NDA 9 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 10 44 -1 1 3 10 43 1 3 4 5 34 1 3 10 12 45 1 3 10 12 42 3 4 5 6 34 4 5 6 8 40 5 6 8 9 12 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK GLY SOL TYPE APEP NAME Glycine # building block (residue, nucleotide, etc.) # RNME GLY # number of atoms, number of preceding exclusions # NMAT NLIN 5 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 3 2 3 4 2 H 21 1 0.31000 1 1 3 3 CA 15 4 0.00000 1 3 4 5 6 # trailing atoms #ATOM ANM IACM MASS CGMICGM 4 C 12 12 0.45000 0 5 O 1 16 -0.45000 1 # bonds # NB 5 # IB JB MCB 1 2 2 1 3 21 3 4 27 4 5 5 4 6 10 # bond angles # NBA 7 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 3 4 5 30 3 4 6 19 5 4 6 33 # improper dihedrals # NIDA 2 # IB JB KB LB MCB 1 -1 3 2 1 4 3 6 5 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 4 44 -1 1 3 4 43 1 3 4 6 45 1 3 4 6 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK HISA SOL TYPE APEP NAME Histidine (protonated at ND1; neutral) # building block (residue, nucleotide, etc.) # RNME HISA # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 13 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 13 14 15 4 CB 15 4 0.00000 1 8 5 6 7 8 9 10 12 13 5 CG 12 12 0.00000 0 7 6 7 8 9 10 11 12 6 ND1 9 14 -0.05000 0 6 7 8 9 10 11 12 7 HD1 21 1 0.31000 0 4 8 10 11 12 8 CD2 12 12 0.00000 0 4 9 10 11 12 9 HD2 20 1 0.14000 0 2 10 12 10 CE1 12 12 0.00000 0 2 11 12 11 HE1 20 1 0.14000 0 1 12 12 NE2 9 14 -0.54000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 13 C 12 12 0.45000 0 14 O 1 16 -0.45000 1 # bonds # NB 15 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 13 27 4 5 27 5 6 10 5 8 10 6 7 2 6 10 10 8 9 3 8 12 10 10 11 3 10 12 10 13 14 5 13 15 10 # bond angles # NBA 23 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 13 13 4 3 13 13 3 4 5 15 4 5 6 37 4 5 8 37 6 5 8 7 5 6 7 36 5 6 10 7 7 6 10 36 5 8 9 36 5 8 12 7 9 8 12 36 6 10 11 36 6 10 12 7 11 10 12 36 8 12 10 7 3 13 14 30 3 13 15 19 14 13 15 33 # improper dihedrals # NIDA 12 # IB JB KB LB MCB 1 -1 3 2 1 3 1 13 4 2 5 6 8 4 1 5 6 10 12 1 5 8 12 10 1 6 5 8 12 1 6 5 10 7 1 6 10 12 8 1 8 5 6 10 1 8 5 12 9 1 10 6 12 11 1 13 3 15 14 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 13 44 -1 1 3 13 43 1 3 4 5 34 1 3 13 15 45 1 3 13 15 42 3 4 5 6 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK HISB SOL TYPE APEP NAME Histidine (protonated at NE2; neutral) # building block (residue, nucleotide, etc.) # RNME HISB # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 13 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 13 14 15 4 CB 15 4 0.00000 1 7 5 6 7 8 9 11 13 5 CG 12 12 0.00000 0 7 6 7 8 9 10 11 12 6 ND1 9 14 -0.54000 0 6 7 8 9 10 11 12 7 CD2 12 12 0.00000 0 5 8 9 10 11 12 8 HD2 20 1 0.14000 0 3 9 11 12 9 CE1 12 12 0.00000 0 3 10 11 12 10 HE1 20 1 0.14000 0 2 11 12 11 NE2 9 14 -0.05000 0 1 12 12 HE2 21 1 0.31000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 13 C 12 12 0.45000 0 14 O 1 16 -0.45000 1 # bonds # NB 15 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 13 27 4 5 27 5 6 10 5 7 10 6 9 10 7 8 3 7 11 10 9 10 3 9 11 10 11 12 2 13 14 5 13 15 10 # bond angles # NBA 23 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 13 13 4 3 13 13 3 4 5 15 4 5 6 37 4 5 7 37 6 5 7 7 5 6 9 7 5 7 8 36 5 7 11 7 8 7 11 36 6 9 10 36 6 9 11 7 10 9 11 36 7 11 9 7 7 11 12 36 9 11 12 36 3 13 14 30 3 13 15 19 14 13 15 33 # improper dihedrals # NIDA 12 # IB JB KB LB MCB 1 -1 3 2 1 3 1 13 4 2 5 6 7 4 1 5 6 9 11 1 5 7 11 9 1 6 5 7 11 1 6 9 11 7 1 7 5 6 9 1 7 5 11 8 1 9 6 11 10 1 11 7 9 12 1 13 3 15 14 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 13 44 -1 1 3 13 43 1 3 4 5 34 1 3 13 15 45 1 3 13 15 42 3 4 5 6 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK HISH SOL TYPE APEP NAME Histidine (protonated at ND1 and NE2; charge +e) # building block (residue, nucleotide, etc.) # RNME HISH # number of atoms, number of preceding exclusions # NMAT NLIN 15 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 14 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 14 15 16 4 CB 15 4 0.00000 1 8 5 6 7 8 9 10 12 14 # Change 54A7->54A8 --- new charges for atoms 5-13 5 CG 12 12 0.14000 0 8 6 7 8 9 10 11 12 13 6 ND1 9 14 -0.03000 0 7 7 8 9 10 11 12 13 7 HD1 21 1 0.32000 0 4 8 10 11 12 8 CD2 12 12 0.00000 0 5 9 10 11 12 13 9 HD2 20 1 0.14000 0 3 10 12 13 10 CE1 12 12 0.00000 0 3 11 12 13 11 HE1 20 1 0.14000 0 2 12 13 12 NE2 9 14 -0.03000 0 1 13 13 HE2 21 1 0.32000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 14 C 12 12 0.45000 0 15 O 1 16 -0.45000 1 # bonds # NB 16 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 14 27 4 5 27 5 6 10 5 8 10 6 7 2 6 10 10 8 9 3 8 12 10 10 11 3 10 12 10 12 13 2 14 15 5 14 16 10 # bond angles # NBA 25 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 14 13 4 3 14 13 3 4 5 15 4 5 6 37 4 5 8 37 6 5 8 7 5 6 7 36 5 6 10 7 7 6 10 36 5 8 9 36 5 8 12 7 9 8 12 36 6 10 11 36 6 10 12 7 11 10 12 36 8 12 10 7 8 12 13 36 10 12 13 36 3 14 15 30 3 14 16 19 15 14 16 33 # improper dihedrals # NIDA 13 # IB JB KB LB MCB 1 -1 3 2 1 3 1 14 4 2 5 6 8 4 1 5 6 10 12 1 5 8 12 10 1 6 5 8 12 1 6 5 10 7 1 6 10 12 8 1 8 5 6 10 1 8 5 12 9 1 10 6 12 11 1 12 8 10 13 1 14 3 16 15 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 14 44 -1 1 3 14 43 1 3 4 5 34 1 3 14 16 45 1 3 14 16 42 3 4 5 6 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK HIS1 SOL TYPE APEP NAME Histidine (coupled to HEME at NE2; neutral) # building block (residue, nucleotide, etc.) # RNME HIS1 # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 13 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 13 14 15 4 CB 15 4 0.00000 1 8 5 6 7 8 9 10 12 13 5 CG 12 12 0.00000 0 8 -1 6 7 8 9 10 11 12 6 ND1 9 14 -0.05000 0 7 -1 7 8 9 10 11 12 7 HD1 21 1 0.31000 0 4 8 10 11 12 8 CD2 12 12 0.00000 0 5 -1 9 10 11 12 9 HD2 20 1 0.14000 0 3 -1 10 12 10 CE1 12 12 0.00000 0 3 -1 11 12 11 HE1 20 1 0.14000 0 2 -1 12 12 NE2 9 14 -0.54000 1 5 -5 -4 -3 -2 -1 # trailing atoms #ATOM ANM IACM MASS CGMICGM 13 C 12 12 0.45000 0 14 O 1 16 -0.45000 1 # bonds # NB 16 # IB JB MCB -1 12 37 1 2 2 1 3 21 3 4 27 3 13 27 4 5 27 5 6 10 5 8 10 6 7 2 6 10 10 8 9 3 8 12 10 10 11 3 10 12 10 13 14 5 13 15 10 # bond angles # NBA 29 # IB JB KB MCB -5 -1 12 2 -4 -1 12 2 -3 -1 12 2 -2 -1 12 2 -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 13 13 4 3 13 13 3 4 5 15 4 5 6 37 4 5 8 37 6 5 8 7 5 6 7 36 5 6 10 7 7 6 10 36 5 8 9 36 5 8 12 7 9 8 12 36 6 10 11 36 6 10 12 7 11 10 12 36 -1 12 8 34 -1 12 10 34 8 12 10 7 3 13 14 30 3 13 15 19 14 13 15 33 # improper dihedrals # NIDA 12 # IB JB KB LB MCB 1 -1 3 2 1 3 1 13 4 2 5 6 8 4 1 5 6 10 12 1 5 8 12 10 1 6 5 8 12 1 6 5 10 7 1 6 10 12 8 1 8 5 6 10 1 8 5 12 9 1 10 6 12 11 1 13 3 15 14 1 # dihedrals # NDA 8 # IB JB KB LB MCB -2 -1 1 3 14 -2 -1 12 8 38 -1 1 3 13 44 -1 1 3 13 43 1 3 4 5 34 1 3 13 15 45 1 3 13 15 42 3 4 5 6 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK HIS2 SOL TYPE APEP NAME Histidine (coupled to HEMC at NE2: neutral) # building block (residue, nucleotide, etc.) # RNME HIS2 # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 13 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 13 14 15 4 CB 15 4 0.00000 1 8 5 6 7 8 9 10 12 13 5 CG 12 12 0.00000 0 8 -1 6 7 8 9 10 11 12 6 ND1 9 14 -0.05000 0 7 -1 7 8 9 10 11 12 7 HD1 21 1 0.31000 0 4 8 10 11 12 8 CD2 12 12 0.00000 0 5 -1 9 10 11 12 9 HD2 20 1 0.14000 0 3 -1 10 12 10 CE1 12 12 0.00000 0 3 -1 11 12 11 HE1 20 1 0.14000 0 2 -1 12 12 NE2 9 14 -0.54000 1 6 -48 -5 -4 -3 -2 -1 # trailing atoms #ATOM ANM IACM MASS CGMICGM 13 C 12 12 0.45000 0 14 O 1 16 -0.45000 1 # bonds # NB 16 # IB JB MCB -1 12 37 1 2 2 1 3 21 3 4 27 3 13 27 4 5 27 5 6 10 5 8 10 6 7 2 6 10 10 8 9 3 8 12 10 10 11 3 10 12 10 13 14 5 13 15 10 # bond angles # NBA 29 # IB JB KB MCB -5 -1 12 2 -4 -1 12 2 -3 -1 12 2 -2 -1 12 2 -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 13 13 4 3 13 13 3 4 5 15 4 5 6 37 4 5 8 37 6 5 8 7 5 6 7 36 5 6 10 7 7 6 10 36 5 8 9 36 5 8 12 7 9 8 12 36 6 10 11 36 6 10 12 7 11 10 12 36 -1 12 8 34 -1 12 10 34 8 12 10 7 3 13 14 30 3 13 15 19 14 13 15 33 # improper dihedrals # NIDA 12 # IB JB KB LB MCB 1 -1 3 2 1 3 1 13 4 2 5 6 8 4 1 5 6 10 12 1 5 8 12 10 1 6 5 8 12 1 6 5 10 7 1 6 10 12 8 1 8 5 6 10 1 8 5 12 9 1 10 6 12 11 1 13 3 15 14 1 # dihedrals # NDA 8 # IB JB KB LB MCB -2 -1 1 3 14 -2 -1 12 8 38 -1 1 3 13 44 -1 1 3 13 43 1 3 4 5 34 1 3 13 15 45 1 3 13 15 42 3 4 5 6 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK HYP SOL TYPE APEP NAME Hydroxyproline # building block (residue, nucleotide, etc.) # RNME HYP # number of atoms, number of preceding exclusions # NMAT NLIN 9 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 7 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 0.00000 1 5 2 3 4 7 8 2 CA 14 3 0.00000 0 6 3 4 7 8 9 10 3 CB 18 4 0.00000 1 4 4 5 7 8 4 CG 14 3 0.26600 0 3 5 6 7 5 OD1 3 16 -0.67400 0 2 6 7 6 HD1 21 1 0.40800 1 0 7 CD2 18 4 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 10 # IB JB MCB 1 2 21 1 7 21 2 3 27 2 8 27 3 4 27 4 5 18 4 7 27 5 6 1 8 9 5 8 10 10 # bond angles # NBA 15 # IB JB KB MCB -1 1 2 31 -1 1 7 31 2 1 7 21 1 2 3 13 1 2 8 13 3 2 8 13 2 3 4 13 3 4 5 13 3 4 7 13 5 4 7 13 4 5 6 12 1 7 4 13 2 8 9 30 2 8 10 19 9 8 10 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 2 7 1 2 1 8 3 2 5 3 7 4 2 8 2 10 9 1 # dihedrals # NDA 10 # IB JB KB LB MCB -2 -1 1 2 14 -1 1 2 8 44 -1 1 2 8 43 2 1 7 4 39 1 2 3 4 34 1 2 8 10 45 1 2 8 10 42 2 3 4 7 34 3 4 5 6 23 3 4 7 1 34 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK ILE SOL TYPE APEP NAME Isoleucine # building block (residue, nucleotide, etc.) # RNME ILE # number of atoms, number of preceding exclusions # NMAT NLIN 9 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 1 6 4 5 6 8 9 10 4 CB 14 3 0.00000 0 4 5 6 7 8 5 CG1 15 4 0.00000 0 2 6 7 6 CG2 16 5 0.00000 0 0 7 CD 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 27 4 6 27 5 7 27 8 9 5 8 10 10 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 15 3 4 6 15 5 4 6 15 4 5 7 15 3 8 9 30 3 8 10 19 9 8 10 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 8 4 2 4 5 6 3 2 8 3 10 9 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 44 -1 1 3 8 43 1 3 4 5 34 1 3 8 10 45 1 3 8 10 42 3 4 5 7 34 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK LEU SOL TYPE APEP NAME Leucine # building block (residue, nucleotide, etc.) # RNME LEU # number of atoms, number of preceding exclusions # NMAT NLIN 9 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 8 9 10 4 CB 15 4 0.00000 1 4 5 6 7 8 5 CG 14 3 0.00000 0 2 6 7 6 CD1 16 5 0.00000 0 1 7 7 CD2 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 27 5 6 27 5 7 27 8 9 5 8 10 10 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 15 4 5 6 15 4 5 7 15 6 5 7 15 3 8 9 30 3 8 10 19 9 8 10 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 8 4 2 4 6 7 5 2 8 3 10 9 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 44 -1 1 3 8 43 1 3 4 5 34 1 3 8 10 45 1 3 8 10 42 3 4 5 6 34 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK LYS SOL TYPE APEP NAME Lysine (deprotonated; neutral) # building block (residue, nucleotide, etc.) # RNME LYS # number of atoms, number of preceding exclusions # NMAT NLIN 12 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 11 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 11 12 13 4 CB 15 4 0.00000 1 3 5 6 11 5 CG 15 4 0.00000 0 2 6 7 6 CD 15 4 0.00000 1 2 7 8 7 CE 15 4 -0.24000 0 3 8 9 10 8 NZ 7 14 -0.64000 0 2 9 10 9 HZ1 21 1 0.44000 0 1 10 10 HZ2 21 1 0.44000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 11 C 12 12 0.45000 0 12 O 1 16 -0.45000 1 # bonds # NB 12 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 11 27 4 5 27 5 6 27 6 7 27 7 8 21 8 9 2 8 10 2 11 12 5 11 13 10 # bond angles # NBA 16 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 11 13 4 3 11 13 3 4 5 15 4 5 6 15 5 6 7 15 6 7 8 15 7 8 9 11 7 8 10 11 9 8 10 10 3 11 12 30 3 11 13 19 12 11 13 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 11 4 2 11 3 13 12 1 # dihedrals # NDA 10 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 11 44 -1 1 3 11 43 1 3 4 5 34 1 3 11 13 45 1 3 11 13 42 3 4 5 6 34 4 5 6 7 34 5 6 7 8 34 6 7 8 9 29 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK LYSH SOL TYPE APEP NAME Lysine (protonated; charge +e) # building block (residue, nucleotide, etc.) # RNME LYSH # number of atoms, number of preceding exclusions # NMAT NLIN 13 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 12 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 12 13 14 4 CB 15 4 0.00000 1 3 5 6 12 5 CG 15 4 0.00000 0 2 6 7 6 CD 15 4 0.00000 1 2 7 8 # Change 54A7->54A8 --- new charges for atoms 7-11 7 CE 15 4 0.20000 0 4 8 9 10 11 8 NZ 8 14 0.05000 0 3 9 10 11 9 HZ1 21 1 0.25000 0 2 10 11 10 HZ2 21 1 0.25000 0 1 11 11 HZ3 21 1 0.25000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 12 C 12 12 0.45000 0 13 O 1 16 -0.45000 1 # bonds # NB 13 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 12 27 4 5 27 5 6 27 6 7 27 7 8 21 8 9 2 8 10 2 8 11 2 12 13 5 12 14 10 # bond angles # NBA 19 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 12 13 4 3 12 13 3 4 5 15 4 5 6 15 5 6 7 15 6 7 8 15 7 8 9 11 7 8 10 11 7 8 11 11 9 8 10 10 9 8 11 10 10 8 11 10 3 12 13 30 3 12 14 19 13 12 14 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 12 4 2 12 3 14 13 1 # dihedrals # NDA 10 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 12 44 -1 1 3 12 43 1 3 4 5 34 1 3 12 14 45 1 3 12 14 42 3 4 5 6 34 4 5 6 7 34 5 6 7 8 34 6 7 8 9 29 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK MET SOL TYPE APEP NAME Methionine # building block (residue, nucleotide, etc.) # RNME MET # number of atoms, number of preceding exclusions # NMAT NLIN 9 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 8 9 10 4 CB 15 4 0.00000 1 3 5 6 8 5 CG 15 4 0.24100 0 2 6 7 6 SD 23 32 -0.48200 0 1 7 7 CE 16 5 0.24100 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 27 5 6 32 6 7 31 8 9 5 8 10 10 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 15 4 5 6 16 5 6 7 4 3 8 9 30 3 8 10 19 9 8 10 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 8 4 2 8 3 10 9 1 # dihedrals # NDA 8 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 44 -1 1 3 8 43 1 3 4 5 34 1 3 8 10 45 1 3 8 10 42 3 4 5 6 34 4 5 6 7 26 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK PHE SOL TYPE APEP NAME Phenylalanine # building block (residue, nucleotide, etc.) # RNME PHE # number of atoms, number of preceding exclusions # NMAT NLIN 17 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 16 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 16 17 18 4 CB 15 4 0.00000 0 8 5 6 7 8 9 10 12 16 5 CG 12 12 0.00000 1 9 6 7 8 9 10 11 12 13 14 6 CD1 12 12 -0.14000 0 8 7 8 9 10 11 12 14 15 7 HD1 20 1 0.14000 1 4 8 10 11 14 8 CD2 12 12 -0.14000 0 6 9 10 12 13 14 15 9 HD2 20 1 0.14000 1 3 12 13 14 10 CE1 12 12 -0.14000 0 5 11 12 13 14 15 11 HE1 20 1 0.14000 1 3 12 14 15 12 CE2 12 12 -0.14000 0 3 13 14 15 13 HE2 20 1 0.14000 1 2 14 15 14 CZ 12 12 -0.14000 0 1 15 15 HZ 20 1 0.14000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 16 C 12 12 0.45000 0 17 O 1 16 -0.45000 1 # bonds # NB 18 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 16 27 4 5 27 5 6 16 5 8 16 6 7 3 6 10 16 8 9 3 8 12 16 10 11 3 10 14 16 12 13 3 12 14 16 14 15 3 16 17 5 16 18 10 # bond angles # NBA 28 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 16 13 4 3 16 13 3 4 5 15 4 5 6 27 4 5 8 27 6 5 8 27 5 6 7 25 5 6 10 27 7 6 10 25 5 8 9 25 5 8 12 27 9 8 12 25 6 10 11 25 6 10 14 27 11 10 14 25 8 12 13 25 8 12 14 27 13 12 14 25 10 14 12 27 10 14 15 25 12 14 15 25 3 16 17 30 3 16 18 19 17 16 18 33 # improper dihedrals # NIDA 15 # IB JB KB LB MCB 1 -1 3 2 1 3 1 16 4 2 5 6 8 4 1 5 6 10 14 1 5 8 12 14 1 6 5 8 12 1 6 5 10 7 1 6 10 14 12 1 8 5 6 10 1 8 5 12 9 1 8 12 14 10 1 11 6 14 10 1 13 8 14 12 1 14 10 12 15 1 16 3 18 17 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 16 44 -1 1 3 16 43 1 3 4 5 34 1 3 16 18 45 1 3 16 18 42 3 4 5 6 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK PRO SOL TYPE APEP NAME Proline # building block (residue, nucleotide, etc.) # RNME PRO # number of atoms, number of preceding exclusions # NMAT NLIN 7 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 5 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 0.00000 1 5 2 3 4 5 6 2 CA 14 3 0.00000 0 6 3 4 5 6 7 8 3 CB 18 4 0.00000 1 3 4 5 6 4 CG 18 4 0.00000 0 1 5 5 CD 18 4 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 12 12 0.45000 0 7 O 1 16 -0.45000 1 # bonds # NB 8 # IB JB MCB 1 2 21 1 5 21 2 3 27 2 6 27 3 4 27 4 5 27 6 7 5 6 8 10 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 31 -1 1 5 31 2 1 5 21 1 2 3 13 1 2 6 13 3 2 6 13 2 3 4 13 3 4 5 13 1 5 4 13 2 6 7 30 2 6 8 19 7 6 8 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 2 5 1 2 1 6 3 2 6 2 8 7 1 # dihedrals # NDA 9 # IB JB KB LB MCB -2 -1 1 2 14 -1 1 2 6 44 -1 1 2 6 43 2 1 5 4 39 1 2 3 4 34 1 2 6 8 45 1 2 6 8 42 2 3 4 5 34 3 4 5 1 34 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK SER SOL TYPE APEP NAME Serine # building block (residue, nucleotide, etc.) # RNME SER # number of atoms, number of preceding exclusions # NMAT NLIN 8 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 7 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 1 5 4 5 7 8 9 4 CB 15 4 0.26600 0 3 5 6 7 5 OG 3 16 -0.67400 0 1 6 6 HG 21 1 0.40800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 7 C 12 12 0.45000 0 8 O 1 16 -0.45000 1 # bonds # NB 8 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 7 27 4 5 18 5 6 1 7 8 5 7 9 10 # bond angles # NBA 11 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 7 13 4 3 7 13 3 4 5 13 4 5 6 12 3 7 8 30 3 7 9 19 8 7 9 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 7 4 2 7 3 9 8 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 44 -1 1 3 7 43 1 3 4 5 34 1 3 7 9 45 1 3 7 9 42 3 4 5 6 23 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK THR SOL TYPE APEP NAME Threonine # building block (residue, nucleotide, etc.) # RNME THR # number of atoms, number of preceding exclusions # NMAT NLIN 9 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 1 6 4 5 7 8 9 10 4 CB 14 3 0.26600 0 4 5 6 7 8 5 OG1 3 16 -0.67400 0 2 6 7 6 HG1 21 1 0.40800 1 0 7 CG2 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 18 4 7 27 5 6 1 8 9 5 8 10 10 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 13 3 4 7 15 5 4 7 15 4 5 6 12 3 8 9 30 3 8 10 19 9 8 10 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 8 4 2 4 5 7 3 2 8 3 10 9 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 44 -1 1 3 8 43 1 3 4 5 34 1 3 8 10 45 1 3 8 10 42 3 4 5 6 23 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK TRP SOL TYPE APEP NAME Tryptophan # building block (residue, nucleotide, etc.) # RNME TRP # number of atoms, number of preceding exclusions # NMAT NLIN 21 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 20 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 20 21 22 4 CB 15 4 0.00000 1 8 5 6 7 8 9 11 12 20 5 CG 12 12 -0.21000 0 10 6 7 8 9 10 11 12 13 14 16 6 CD1 12 12 -0.14000 0 7 7 8 9 10 11 12 14 7 HD1 20 1 0.14000 0 4 8 9 10 11 8 CD2 12 12 0.00000 0 10 9 10 11 12 13 14 15 16 17 18 9 NE1 9 14 -0.10000 0 6 10 11 12 14 15 18 10 HE1 21 1 0.31000 0 2 11 14 11 CE2 12 12 0.00000 1 7 12 13 14 15 16 18 19 12 CE3 12 12 -0.14000 0 6 13 14 16 17 18 19 13 HE3 20 1 0.14000 1 3 16 17 18 14 CZ2 12 12 -0.14000 0 5 15 16 17 18 19 15 HZ2 20 1 0.14000 1 3 16 18 19 16 CZ3 12 12 -0.14000 0 3 17 18 19 17 HZ3 20 1 0.14000 1 2 18 19 18 CH2 12 12 -0.14000 0 1 19 19 HH2 20 1 0.14000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 20 C 12 12 0.45000 0 21 O 1 16 -0.45000 1 # bonds # NB 23 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 20 27 4 5 27 5 6 10 5 8 16 6 7 3 6 9 10 8 11 16 8 12 16 9 10 2 9 11 10 11 14 16 12 13 3 12 16 16 14 15 3 14 18 16 16 17 3 16 18 16 18 19 3 20 21 5 20 22 10 # bond angles # NBA 37 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 20 13 4 3 20 13 3 4 5 15 4 5 6 37 4 5 8 37 6 5 8 7 5 6 7 36 5 6 9 7 7 6 9 36 5 8 11 7 5 8 12 39 11 8 12 27 6 9 10 36 6 9 11 7 10 9 11 36 8 11 9 7 8 11 14 27 9 11 14 39 8 12 13 25 8 12 16 27 13 12 16 25 11 14 15 25 11 14 18 27 15 14 18 25 12 16 17 25 12 16 18 27 17 16 18 25 14 18 16 27 14 18 19 25 16 18 19 25 3 20 21 30 3 20 22 19 21 20 22 33 # improper dihedrals # NIDA 23 # IB JB KB LB MCB 1 -1 3 2 1 3 1 20 4 2 5 6 8 4 1 5 6 9 11 1 5 8 11 9 1 6 5 8 11 1 6 5 9 7 1 6 9 11 8 1 8 5 6 9 1 8 11 12 5 1 8 11 14 18 1 8 12 16 18 1 9 6 11 10 1 11 8 12 16 1 11 8 14 9 1 11 14 18 16 1 12 8 11 14 1 12 8 16 13 1 12 16 18 14 1 14 11 18 15 1 16 12 18 17 1 18 14 16 19 1 20 3 22 21 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 20 44 -1 1 3 20 43 1 3 4 5 34 1 3 20 22 45 1 3 20 22 42 3 4 5 8 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK TYR SOL TYPE APEP NAME Tyrosine # building block (residue, nucleotide, etc.) # RNME TYR # number of atoms, number of preceding exclusions # NMAT NLIN 18 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 17 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 17 18 19 4 CB 15 4 0.00000 0 8 5 6 7 8 9 10 12 17 5 CG 12 12 0.00000 1 9 6 7 8 9 10 11 12 13 14 6 CD1 12 12 -0.14000 0 8 7 8 9 10 11 12 14 15 7 HD1 20 1 0.14000 1 4 8 10 11 14 8 CD2 12 12 -0.14000 0 6 9 10 12 13 14 15 9 HD2 20 1 0.14000 1 3 12 13 14 10 CE1 12 12 -0.14000 0 5 11 12 13 14 15 11 HE1 20 1 0.14000 1 3 12 14 15 12 CE2 12 12 -0.14000 0 3 13 14 15 13 HE2 20 1 0.14000 1 2 14 15 14 CZ 12 12 0.20300 0 2 15 16 15 OH 3 16 -0.61100 0 1 16 16 HH 21 1 0.40800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 17 C 12 12 0.45000 0 18 O 1 16 -0.45000 1 # bonds # NB 19 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 17 27 4 5 27 5 6 16 5 8 16 6 7 3 6 10 16 8 9 3 8 12 16 10 11 3 10 14 16 12 13 3 12 14 16 14 15 13 15 16 1 17 18 5 17 19 10 # bond angles # NBA 29 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 17 13 4 3 17 13 3 4 5 15 4 5 6 27 4 5 8 27 6 5 8 27 5 6 7 25 5 6 10 27 7 6 10 25 5 8 9 25 5 8 12 27 9 8 12 25 6 10 11 25 6 10 14 27 11 10 14 25 8 12 13 25 8 12 14 27 13 12 14 25 10 14 12 27 10 14 15 27 12 14 15 27 14 15 16 12 3 17 18 30 3 17 19 19 18 17 19 33 # improper dihedrals # NIDA 15 # IB JB KB LB MCB 1 -1 3 2 1 3 1 17 4 2 5 6 8 4 1 5 6 10 14 1 5 8 12 14 1 6 5 8 12 1 6 5 10 7 1 6 10 14 12 1 8 5 6 10 1 8 5 12 9 1 8 12 14 10 1 11 6 14 10 1 13 8 14 12 1 14 10 12 15 1 17 3 19 18 1 # dihedrals # NDA 8 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 17 44 -1 1 3 17 43 1 3 4 5 34 1 3 17 19 45 1 3 17 19 42 3 4 5 6 40 10 14 15 16 11 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK VAL SOL TYPE APEP NAME Valine # building block (residue, nucleotide, etc.) # RNME VAL # number of atoms, number of preceding exclusions # NMAT NLIN 8 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 7 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 6 4 5 6 7 8 9 4 CB 14 3 0.00000 0 3 5 6 7 5 CG1 16 5 0.00000 0 1 6 6 CG2 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 7 C 12 12 0.45000 0 8 O 1 16 -0.45000 1 # bonds # NB 8 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 7 27 4 5 27 4 6 27 7 8 5 7 9 10 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 7 13 4 3 7 13 3 4 5 15 3 4 6 15 5 4 6 15 3 7 8 30 3 7 9 19 8 7 9 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 7 4 2 3 5 6 4 2 7 3 9 8 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 44 -1 1 3 7 43 1 3 4 5 34 1 3 7 9 45 1 3 7 9 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK DALA SOL TYPE APEP NAME D-Alanine # building block (residue, nucleotide, etc.) # RNME DALA # number of atoms, number of preceding exclusions # NMAT NLIN 6 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 5 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 4 4 5 6 7 4 CB 16 5 0.00000 1 1 5 # trailing atoms #ATOM ANM IACM MASS CGMICGM 5 C 12 12 0.45000 0 6 O 1 16 -0.45000 1 # bonds # NB 6 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 5 27 5 6 5 5 7 10 # bond angles # NBA 9 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 5 13 4 3 5 13 3 5 6 30 3 5 7 19 6 5 7 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 4 1 5 3 2 5 3 7 6 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 5 44 -1 1 3 5 43 1 3 5 7 45 1 3 5 7 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK ABU SOL TYPE APEP NAME L-2-amino-butanoic acid # building block (residue, nucleotide, etc.) # RNME ABU # number of atoms, number of preceding exclusions # NMAT NLIN 7 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 6 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 6 7 8 4 CB 15 4 0.00000 0 2 5 6 5 CG 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 12 12 0.45000 0 7 O 1 16 -0.45000 1 # bonds # NB 7 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 6 27 4 5 27 6 7 5 6 8 10 # bond angles # NBA 10 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 6 13 4 3 6 13 3 4 5 15 3 6 7 30 3 6 8 19 7 6 8 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 6 4 2 6 3 8 7 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 6 44 -1 1 3 6 43 1 3 4 5 34 1 3 6 8 45 1 3 6 8 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK AIB SOL TYPE APEP NAME 2-aminoisobutyric acid # building block (residue, nucleotide, etc.) # RNME AIB # number of atoms, number of preceding exclusions # NMAT NLIN 7 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 5 2 3 4 5 6 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 6 7 8 4 CB 16 5 0.00000 0 2 5 6 5 CG 16 5 0.00000 1 1 6 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 12 12 0.45000 0 7 O 1 16 -0.45000 1 # bonds # NB 7 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 5 27 3 6 27 6 7 5 6 8 10 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 5 13 1 3 6 13 4 3 5 13 4 3 6 13 5 3 6 13 3 6 7 30 3 6 8 19 7 6 8 33 # improper dihedrals # NIDA 2 # IB JB KB LB MCB 1 -1 3 2 1 6 3 8 7 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 6 44 -1 1 3 6 43 1 3 6 8 45 1 3 6 8 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK MEBMT SOL TYPE APEP NAME (4R)-4-[(E)-2-butanyl]-4,N-dimethyl-L-threonine # building block (residue, nucleotide, etc.) # RNME MEBMT # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 0.00000 0 4 2 3 4 13 2 CN 16 5 0.00000 1 1 3 3 CA 14 3 0.00000 1 6 4 5 7 13 14 15 4 CB 14 3 0.26600 0 6 5 6 7 8 9 13 5 OG1 3 16 -0.67400 0 2 6 7 6 HG1 21 1 0.40800 1 0 7 CG2 14 3 0.00000 0 3 8 9 10 8 CD1 16 5 0.00000 0 1 9 9 CD2 15 4 0.00000 1 2 10 11 10 CE 19 3 0.00000 0 2 11 12 11 CZ 19 3 0.00000 0 1 12 12 CH 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 13 C 12 12 0.45000 0 14 O 1 16 -0.45000 1 # bonds # NB 14 # IB JB MCB 1 2 21 1 3 21 3 4 27 3 13 27 4 5 18 4 7 27 5 6 1 7 8 27 7 9 27 9 10 27 10 11 10 11 12 27 13 14 5 13 15 10 # bond angles # NBA 19 # IB JB KB MCB -1 1 2 22 -1 1 3 31 2 1 3 30 1 3 4 13 1 3 13 13 4 3 13 13 3 4 5 13 3 4 7 15 5 4 7 15 4 5 6 12 4 7 8 15 4 7 9 15 8 7 9 15 7 9 10 15 9 10 11 27 10 11 12 27 3 13 14 30 3 13 15 19 14 13 15 33 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 1 -1 3 2 1 3 1 13 4 2 4 5 7 3 2 7 8 9 4 2 13 3 15 14 1 # dihedrals # NDA 11 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 13 44 -1 1 3 13 43 1 3 4 7 34 1 3 13 15 45 1 3 13 15 42 3 4 5 6 23 3 4 7 9 34 4 7 9 10 34 7 9 10 11 40 9 10 11 12 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK MELEU SOL TYPE APEP NAME N-methyl-L-leucine # building block (residue, nucleotide, etc.) # RNME MELEU # number of atoms, number of preceding exclusions # NMAT NLIN 9 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 0.00000 0 4 2 3 4 8 2 CN 16 5 0.00000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 8 9 10 4 CB 15 4 0.00000 1 4 5 6 7 8 5 CG 14 3 0.00000 0 2 6 7 6 CD1 16 5 0.00000 0 1 7 7 CD2 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 21 1 3 21 3 4 27 3 8 27 4 5 27 5 6 27 5 7 27 8 9 5 8 10 10 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 22 -1 1 3 31 2 1 3 30 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 15 4 5 6 15 4 5 7 15 6 5 7 15 3 8 9 30 3 8 10 19 9 8 10 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 8 4 2 4 6 7 5 2 8 3 10 9 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 44 -1 1 3 8 43 1 3 4 5 34 1 3 8 10 45 1 3 8 10 42 3 4 5 6 34 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK MEVAL SOL TYPE APEP NAME N-methyl-L-valine # building block (residue, nucleotide, etc.) # RNME MEVAL # number of atoms, number of preceding exclusions # NMAT NLIN 8 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 0.00000 0 4 2 3 4 7 2 CN 16 5 0.00000 1 1 3 3 CA 14 3 0.00000 0 6 4 5 6 7 8 9 4 CB 14 3 0.00000 0 3 5 6 7 5 CG1 16 5 0.00000 0 1 6 6 CG2 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 7 C 12 12 0.45000 0 8 O 1 16 -0.45000 1 # bonds # NB 8 # IB JB MCB 1 2 21 1 3 21 3 4 27 3 7 27 4 5 27 4 6 27 7 8 5 7 9 10 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 22 -1 1 3 31 2 1 3 30 1 3 4 13 1 3 7 13 4 3 7 13 3 4 5 15 3 4 6 15 5 4 6 15 3 7 8 30 3 7 9 19 8 7 9 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 7 4 2 3 5 6 4 2 7 3 9 8 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 44 -1 1 3 7 43 1 3 4 5 34 1 3 7 9 45 1 3 7 9 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK SAR SOL TYPE APEP NAME Sarcosine or N-methylglycine # building block (residue, nucleotide, etc.) # RNME SAR # number of atoms, number of preceding exclusions # NMAT NLIN 5 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 0.00000 0 3 2 3 4 2 CN 16 5 0.00000 1 1 3 3 CA 15 4 0.00000 1 3 4 5 6 # trailing atoms #ATOM ANM IACM MASS CGMICGM 4 C 12 12 0.45000 0 5 O 1 16 -0.45000 1 # bonds # NB 5 # IB JB MCB 1 2 21 1 3 21 3 4 27 4 5 5 4 6 10 # bond angles # NBA 7 # IB JB KB MCB -1 1 2 22 -1 1 3 31 2 1 3 30 1 3 4 13 3 4 5 30 3 4 6 19 5 4 6 33 # improper dihedrals # NIDA 2 # IB JB KB LB MCB 1 -1 3 2 1 4 3 6 5 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 4 44 -1 1 3 4 43 1 3 4 6 45 1 3 4 6 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK DADE SOL TYPE DNUC NAME 2-deoxyadenosine 5-phosphoric acid (DNA, charge -e) # building block (residue, nucleotide, etc.) # RNME DADE # number of atoms, number of preceding exclusions # NMAT NLIN 25 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 30 31 0.99000 0 4 2 3 4 5 2 O1P 2 16 -0.63500 0 2 3 4 3 O2P 2 16 -0.63500 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 15 4 0.00000 1 3 6 7 24 6 C4* 14 3 0.16000 0 5 7 8 23 24 25 7 O4* 3 16 -0.36000 0 4 8 9 23 24 8 C1* 14 3 0.20000 1 9 9 10 11 19 20 21 22 23 24 9 N9 9 14 -0.20000 0 9 10 11 12 15 19 20 21 22 23 10 C4 12 12 0.20000 1 10 11 12 13 14 15 16 19 20 21 22 11 N3 9 14 -0.54000 0 7 12 13 14 15 19 20 21 12 C2 12 12 0.44000 0 5 13 14 15 16 19 13 H2 20 1 0.10000 1 2 14 15 14 N1 9 14 -0.54000 0 4 15 16 19 20 15 C6 12 12 0.54000 1 6 16 17 18 19 20 21 16 N6 7 14 -0.83000 0 4 17 18 19 20 17 H61 21 1 0.41500 0 2 18 20 18 H62 21 1 0.41500 1 1 20 19 C5 12 12 0.00000 0 3 20 21 22 20 N7 9 14 -0.54000 0 2 21 22 21 C8 12 12 0.44000 0 1 22 22 H8 20 1 0.10000 1 0 23 C2* 18 4 0.00000 0 2 24 25 # trailing atoms #ATOM ANM IACM MASS CGMICGM 24 C3* 14 3 0.00000 1 25 O3* 3 16 -0.36000 0 # bonds # NB 28 # IB JB MCB 1 2 24 1 3 24 1 4 28 4 5 20 5 6 26 6 7 20 6 24 26 7 8 20 8 9 22 8 23 26 9 10 10 9 21 10 10 11 12 10 19 16 11 12 7 12 13 3 12 14 7 14 15 12 15 16 9 15 19 16 16 17 2 16 18 2 19 20 10 20 21 10 21 22 3 23 24 26 24 25 20 25 26 28 # bond angles # NBA 44 # IB JB KB MCB 0 1 2 14 0 1 3 14 0 1 4 5 2 1 3 29 2 1 4 14 3 1 4 14 1 4 5 26 4 5 6 9 5 6 7 9 5 6 24 8 7 6 24 9 6 7 8 10 7 8 9 9 7 8 23 9 9 8 23 9 8 9 10 37 8 9 21 37 10 9 21 7 9 10 11 39 9 10 19 7 11 10 19 27 10 11 12 27 11 12 13 25 11 12 14 27 13 12 14 25 12 14 15 27 14 15 16 27 14 15 19 27 16 15 19 27 15 16 17 23 15 16 18 23 17 16 18 24 10 19 15 27 10 19 20 7 15 19 20 39 19 20 21 7 9 21 20 7 9 21 22 36 20 21 22 36 8 23 24 8 6 24 23 8 6 24 25 9 23 24 25 9 24 25 26 26 # improper dihedrals # NIDA 21 # IB JB KB LB MCB 8 10 21 9 1 9 10 19 20 1 10 9 11 19 1 10 9 21 20 1 10 11 12 14 1 10 19 20 21 1 11 10 19 15 1 11 12 14 15 1 12 11 13 14 1 12 14 15 19 1 14 15 19 10 1 16 14 19 15 1 16 17 18 15 1 19 10 11 12 1 19 15 20 10 1 19 20 21 9 1 21 9 10 19 1 21 9 20 22 1 23 7 9 8 2 24 5 7 6 2 24 23 25 6 2 # dihedrals # NDA 23 # IB JB KB LB MCB -1 0 1 4 20 -1 0 1 4 27 0 1 4 5 20 0 1 4 5 27 1 4 5 6 7 1 4 5 6 22 4 5 6 7 8 4 5 6 7 25 4 5 6 24 17 4 5 6 24 34 24 6 7 8 29 5 6 24 23 34 5 6 24 25 17 7 6 24 23 17 7 6 24 25 18 6 7 8 23 29 7 8 9 10 16 7 8 23 24 17 7 8 23 24 34 19 15 16 17 14 8 23 24 6 34 8 23 24 25 17 6 24 25 26 29 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK DGUA SOL TYPE DNUC NAME 2-deoxyguanosine 5-phosphoric acid (DNA, charge -e) # building block (residue, nucleotide, etc.) # RNME DGUA # number of atoms, number of preceding exclusions # NMAT NLIN 26 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 30 31 0.99000 0 4 2 3 4 5 2 O1P 2 16 -0.63500 0 2 3 4 3 O2P 2 16 -0.63500 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 15 4 0.00000 1 3 6 7 25 6 C4* 14 3 0.16000 0 5 7 8 24 25 26 7 O4* 3 16 -0.36000 0 4 8 9 24 25 8 C1* 14 3 0.20000 1 9 9 10 11 20 21 22 23 24 25 9 N9 9 14 -0.20000 0 9 10 11 12 18 20 21 22 23 24 10 C4 12 12 0.20000 1 10 11 12 13 16 18 19 20 21 22 23 11 N3 9 14 -0.54000 0 8 12 13 16 17 18 20 21 22 12 C2 12 12 0.54000 1 8 13 14 15 16 17 18 19 20 13 N2 7 14 -0.83000 0 5 14 15 16 17 18 14 H21 21 1 0.41500 0 1 15 15 H22 21 1 0.41500 1 0 16 N1 9 14 -0.31000 0 5 17 18 19 20 21 17 H1 21 1 0.31000 1 3 18 19 20 18 C6 12 12 0.45000 0 4 19 20 21 22 19 O6 1 16 -0.45000 1 2 20 21 20 C5 12 12 0.00000 0 3 21 22 23 21 N7 9 14 -0.54000 0 2 22 23 22 C8 12 12 0.44000 0 1 23 23 H8 20 1 0.10000 1 0 24 C2* 18 4 0.00000 0 2 25 26 # trailing atoms #ATOM ANM IACM MASS CGMICGM 25 C3* 14 3 0.00000 1 26 O3* 3 16 -0.36000 0 # bonds # NB 29 # IB JB MCB 1 2 24 1 3 24 1 4 28 4 5 20 5 6 26 6 7 20 6 25 26 7 8 20 8 9 22 8 24 26 9 10 10 9 22 10 10 11 12 10 20 16 11 12 12 12 13 9 12 16 17 13 14 2 13 15 2 16 17 2 16 18 17 18 19 5 18 20 16 20 21 10 21 22 10 22 23 3 24 25 26 25 26 20 26 27 28 # bond angles # NBA 46 # IB JB KB MCB 0 1 2 14 0 1 3 14 0 1 4 5 2 1 3 29 2 1 4 14 3 1 4 14 1 4 5 26 4 5 6 9 5 6 7 9 5 6 25 8 7 6 25 9 6 7 8 10 7 8 9 9 7 8 24 9 9 8 24 9 8 9 10 37 8 9 22 37 10 9 22 7 9 10 11 39 9 10 20 7 11 10 20 27 10 11 12 27 11 12 13 27 11 12 16 27 13 12 16 27 12 13 14 23 12 13 15 23 14 13 15 24 12 16 17 25 12 16 18 27 17 16 18 25 16 18 19 27 16 18 20 27 19 18 20 27 10 20 18 27 10 20 21 7 18 20 21 39 20 21 22 7 9 22 21 7 9 22 23 36 21 22 23 36 8 24 25 8 6 25 24 8 6 25 26 9 24 25 26 9 25 26 27 26 # improper dihedrals # NIDA 22 # IB JB KB LB MCB 8 10 22 9 1 9 10 20 21 1 10 9 11 20 1 10 9 22 21 1 10 11 12 16 1 10 20 21 22 1 11 10 20 18 1 11 12 16 18 1 12 16 18 20 1 13 11 16 12 1 13 14 15 12 1 16 18 20 10 1 17 12 18 16 1 19 16 20 18 1 20 10 11 12 1 20 18 21 10 1 20 21 22 9 1 22 9 10 20 1 22 9 21 23 1 24 7 9 8 2 25 5 7 6 2 25 24 26 6 2 # dihedrals # NDA 23 # IB JB KB LB MCB -1 0 1 4 20 -1 0 1 4 27 0 1 4 5 20 0 1 4 5 27 1 4 5 6 7 1 4 5 6 22 4 5 6 7 8 4 5 6 7 25 4 5 6 25 17 4 5 6 25 34 25 6 7 8 29 5 6 25 24 34 5 6 25 26 17 7 6 25 24 17 7 6 25 26 18 6 7 8 24 29 7 8 9 10 16 7 8 24 25 17 7 8 24 25 34 11 12 13 14 14 8 24 25 6 34 8 24 25 26 17 6 25 26 27 29 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK DCYT SOL TYPE DNUC NAME 2-deoxycitidine 5-phosphoric acid (DNA, charge -e) # building block (residue, nucleotide, etc.) # RNME DCYT # number of atoms, number of preceding exclusions # NMAT NLIN 23 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 30 31 0.99000 0 4 2 3 4 5 2 O1P 2 16 -0.63500 0 2 3 4 3 O2P 2 16 -0.63500 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 15 4 0.00000 1 3 6 7 22 6 C4* 14 3 0.16000 0 5 7 8 21 22 23 7 O4* 3 16 -0.36000 0 4 8 9 21 22 8 C1* 14 3 0.20000 1 9 9 10 11 12 13 14 19 21 22 9 N1 9 14 -0.20000 0 9 10 11 12 13 14 15 19 20 21 10 C6 12 12 0.10000 0 8 11 12 13 14 15 16 19 20 11 H6 20 1 0.10000 1 4 12 15 19 20 12 C2 12 12 0.45000 0 5 13 14 15 16 19 13 O2 1 16 -0.45000 1 2 14 15 14 N3 9 14 -0.54000 0 4 15 16 19 20 15 C4 12 12 0.54000 1 5 16 17 18 19 20 16 N4 7 14 -0.83000 0 4 17 18 19 20 17 H41 21 1 0.41500 0 1 18 18 H42 21 1 0.41500 1 0 19 C5 12 12 -0.10000 0 1 20 20 H5 20 1 0.10000 1 0 21 C2* 18 4 0.00000 0 2 22 23 # trailing atoms #ATOM ANM IACM MASS CGMICGM 22 C3* 14 3 0.00000 1 23 O3* 3 16 -0.36000 0 # bonds # NB 25 # IB JB MCB 1 2 24 1 3 24 1 4 28 4 5 20 5 6 26 6 7 20 6 22 26 7 8 20 8 9 23 8 21 26 9 10 17 9 12 17 10 11 3 10 19 16 12 13 5 12 14 12 14 15 12 15 16 9 15 19 16 16 17 2 16 18 2 19 20 3 21 22 26 22 23 20 23 24 28 # bond angles # NBA 39 # IB JB KB MCB 0 1 2 14 0 1 3 14 0 1 4 5 2 1 3 29 2 1 4 14 3 1 4 14 1 4 5 26 4 5 6 9 5 6 7 9 5 6 22 8 7 6 22 9 6 7 8 10 7 8 9 9 7 8 21 9 9 8 21 8 8 9 10 27 8 9 12 27 10 9 12 27 9 10 11 25 9 10 19 27 11 10 19 25 9 12 13 27 9 12 14 27 13 12 14 27 12 14 15 27 14 15 16 27 14 15 19 27 16 15 19 27 15 16 17 23 15 16 18 23 17 16 18 24 10 19 15 27 10 19 20 25 15 19 20 25 8 21 22 8 6 22 21 8 6 22 23 9 21 22 23 9 22 23 24 26 # improper dihedrals # NIDA 15 # IB JB KB LB MCB 9 10 12 8 1 9 10 19 15 1 9 12 14 15 1 10 9 12 14 1 10 9 19 11 1 12 9 10 19 1 12 14 15 19 1 13 9 14 12 1 14 15 19 10 1 16 14 19 15 1 16 17 18 15 1 19 10 15 20 1 21 7 9 8 2 22 5 7 6 2 22 21 23 6 2 # dihedrals # NDA 23 # IB JB KB LB MCB -1 0 1 4 20 -1 0 1 4 27 0 1 4 5 20 0 1 4 5 27 1 4 5 6 7 1 4 5 6 22 4 5 6 7 8 4 5 6 7 25 4 5 6 22 17 4 5 6 22 34 22 6 7 8 29 5 6 22 21 34 5 6 22 23 17 7 6 22 21 17 7 6 22 23 18 6 7 8 21 29 7 8 9 12 16 7 8 21 22 17 7 8 21 22 34 14 15 16 17 14 8 21 22 6 34 8 21 22 23 17 6 22 23 24 29 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK DTHY SOL TYPE DNUC NAME 2-deoxythymidine 5-phosphoric acid (DNA, charge -e) # building block (residue, nucleotide, etc.) # RNME DTHY # number of atoms, number of preceding exclusions # NMAT NLIN 22 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 30 31 0.99000 0 4 2 3 4 5 2 O1P 2 16 -0.63500 0 2 3 4 3 O2P 2 16 -0.63500 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 15 4 0.00000 1 3 6 7 21 6 C4* 14 3 0.16000 0 5 7 8 20 21 22 7 O4* 3 16 -0.36000 0 4 8 9 20 21 8 C1* 14 3 0.20000 1 9 9 10 11 12 13 14 18 20 21 9 N1 9 14 -0.20000 0 10 10 11 12 13 14 15 16 18 19 20 10 C6 12 12 0.10000 0 8 11 12 13 14 16 17 18 19 11 H6 20 1 0.10000 1 4 12 16 18 19 12 C2 12 12 0.45000 0 6 13 14 15 16 17 18 13 O2 1 16 -0.45000 1 3 14 15 16 14 N3 9 14 -0.31000 0 5 15 16 17 18 19 15 H3 21 1 0.31000 1 3 16 17 18 16 C4 12 12 0.45000 0 3 17 18 19 17 O4 1 16 -0.45000 1 2 18 19 18 C5 12 12 0.00000 0 1 19 19 C5M 16 5 0.00000 1 0 20 C2* 18 4 0.00000 0 2 21 22 # trailing atoms #ATOM ANM IACM MASS CGMICGM 21 C3* 14 3 0.00000 1 22 O3* 3 16 -0.36000 0 # bonds # NB 24 # IB JB MCB 1 2 24 1 3 24 1 4 28 4 5 20 5 6 26 6 7 20 6 21 26 7 8 20 8 9 23 8 20 26 9 10 17 9 12 17 10 11 3 10 18 16 12 13 5 12 14 17 14 15 2 14 16 17 16 17 5 16 18 16 18 19 27 20 21 26 21 22 20 22 23 28 # bond angles # NBA 38 # IB JB KB MCB 0 1 2 14 0 1 3 14 0 1 4 5 2 1 3 29 2 1 4 14 3 1 4 14 1 4 5 26 4 5 6 9 5 6 7 9 5 6 21 8 7 6 21 9 6 7 8 10 7 8 9 9 7 8 20 9 9 8 20 8 8 9 10 27 8 9 12 27 10 9 12 27 9 10 11 25 9 10 18 27 11 10 18 25 9 12 13 27 9 12 14 27 13 12 14 27 12 14 15 25 12 14 16 27 15 14 16 25 14 16 17 27 14 16 18 27 17 16 18 27 10 18 16 27 10 18 19 27 16 18 19 27 8 20 21 8 6 21 20 8 6 21 22 9 20 21 22 9 21 22 23 26 # improper dihedrals # NIDA 15 # IB JB KB LB MCB 9 10 12 8 1 9 10 18 16 1 9 12 14 16 1 10 9 12 14 1 10 9 18 11 1 12 9 10 18 1 12 14 16 18 1 13 9 14 12 1 14 16 18 10 1 15 12 16 14 1 17 14 18 16 1 18 10 16 19 1 20 7 9 8 2 21 5 7 6 2 21 20 22 6 2 # dihedrals # NDA 22 # IB JB KB LB MCB -1 0 1 4 20 -1 0 1 4 27 0 1 4 5 20 0 1 4 5 27 1 4 5 6 7 1 4 5 6 22 4 5 6 7 8 4 5 6 7 25 4 5 6 21 17 4 5 6 21 34 21 6 7 8 29 5 6 21 20 34 5 6 21 22 17 7 6 21 20 17 7 6 21 22 18 6 7 8 20 29 7 8 9 12 16 7 8 20 21 17 7 8 20 21 34 8 20 21 6 34 8 20 21 22 17 6 21 22 23 29 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK ADE SOL TYPE RNUC NAME adenosine 5-phosphoric acid (RNA, charge -e) # building block (residue, nucleotide, etc.) # RNME ADE # number of atoms, number of preceding exclusions # NMAT NLIN 27 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 30 31 0.99000 0 4 2 3 4 5 2 O1P 2 16 -0.63500 0 2 3 4 3 O2P 2 16 -0.63500 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 15 4 0.00000 1 3 6 7 26 6 C4* 14 3 0.16000 0 5 7 8 23 26 27 7 O4* 3 16 -0.36000 0 4 8 9 23 26 8 C1* 14 3 0.20000 1 10 9 10 11 19 20 21 22 23 24 26 9 N9 9 14 -0.20000 0 9 10 11 12 15 19 20 21 22 23 10 C4 12 12 0.20000 1 10 11 12 13 14 15 16 19 20 21 22 11 N3 9 14 -0.54000 0 7 12 13 14 15 19 20 21 12 C2 12 12 0.44000 0 5 13 14 15 16 19 13 H2 20 1 0.10000 1 2 14 15 14 N1 9 14 -0.54000 0 4 15 16 19 20 15 C6 12 12 0.54000 1 6 16 17 18 19 20 21 16 N6 7 14 -0.83000 0 4 17 18 19 20 17 H61 21 1 0.41500 0 2 18 20 18 H62 21 1 0.41500 1 1 20 19 C5 12 12 0.00000 0 3 20 21 22 20 N7 9 14 -0.54000 0 2 21 22 21 C8 12 12 0.44000 0 1 22 22 H8 20 1 0.10000 1 0 23 C2* 14 3 0.15000 0 4 24 25 26 27 24 O2* 3 16 -0.54800 0 2 25 26 25 H2* 21 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 26 C3* 14 3 0.00000 1 27 O3* 3 16 -0.36000 0 # bonds # NB 30 # IB JB MCB 1 2 24 1 3 24 1 4 28 4 5 20 5 6 26 6 7 20 6 26 26 7 8 20 8 9 22 8 23 26 9 10 10 9 21 10 10 11 12 10 19 16 11 12 7 12 13 3 12 14 7 14 15 12 15 16 9 15 19 16 16 17 2 16 18 2 19 20 10 20 21 10 21 22 3 23 24 20 23 26 26 24 25 1 26 27 20 27 28 28 # bond angles # NBA 47 # IB JB KB MCB 0 1 2 14 0 1 3 14 0 1 4 5 2 1 3 29 2 1 4 14 3 1 4 14 1 4 5 26 4 5 6 9 5 6 7 9 5 6 26 8 7 6 26 9 6 7 8 10 7 8 9 9 7 8 23 9 9 8 23 9 8 9 10 37 8 9 21 37 10 9 21 7 9 10 11 39 9 10 19 7 11 10 19 27 10 11 12 27 11 12 13 25 11 12 14 27 13 12 14 25 12 14 15 27 14 15 16 27 14 15 19 27 16 15 19 27 15 16 17 23 15 16 18 23 17 16 18 24 10 19 15 27 10 19 20 7 15 19 20 39 19 20 21 7 9 21 20 7 9 21 22 36 20 21 22 36 8 23 24 9 8 23 26 8 24 23 26 9 23 24 25 12 6 26 23 8 6 26 27 9 23 26 27 9 26 27 28 26 # improper dihedrals # NIDA 22 # IB JB KB LB MCB 8 10 21 9 1 9 10 19 20 1 10 9 11 19 1 10 9 21 20 1 10 11 12 14 1 10 19 20 21 1 11 10 19 15 1 11 12 14 15 1 12 11 13 14 1 12 14 15 19 1 14 15 19 10 1 16 14 19 15 1 16 17 18 15 1 19 10 11 12 1 19 15 20 10 1 19 20 21 9 1 21 9 10 19 1 21 9 20 22 1 23 7 9 8 2 23 24 26 8 2 26 5 7 6 2 26 23 27 6 2 # dihedrals # NDA 28 # IB JB KB LB MCB -1 0 1 4 20 -1 0 1 4 27 0 1 4 5 20 0 1 4 5 27 1 4 5 6 7 1 4 5 6 22 4 5 6 7 8 4 5 6 7 25 4 5 6 26 17 4 5 6 26 34 26 6 7 8 29 5 6 26 23 34 5 6 26 27 17 7 6 26 23 17 7 6 26 27 18 6 7 8 23 29 7 8 9 10 16 7 8 23 24 18 7 8 23 26 17 7 8 23 26 34 9 8 23 24 17 19 15 16 17 14 8 23 24 25 23 8 23 26 6 34 8 23 26 27 17 24 23 26 6 17 24 23 26 27 18 6 26 27 28 29 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK GUA SOL TYPE RNUC NAME guanosine 5-phosphoric acid (RNA, charge -e) # building block (residue, nucleotide, etc.) # RNME GUA # number of atoms, number of preceding exclusions # NMAT NLIN 28 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 30 31 0.99000 0 4 2 3 4 5 2 O1P 2 16 -0.63500 0 2 3 4 3 O2P 2 16 -0.63500 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 15 4 0.00000 1 3 6 7 27 6 C4* 14 3 0.16000 0 5 7 8 24 27 28 7 O4* 3 16 -0.36000 0 4 8 9 24 27 8 C1* 14 3 0.20000 1 10 9 10 11 20 21 22 23 24 25 27 9 N9 9 14 -0.20000 0 9 10 11 12 18 20 21 22 23 24 10 C4 12 12 0.20000 1 10 11 12 13 16 18 19 20 21 22 23 11 N3 9 14 -0.54000 0 8 12 13 16 17 18 20 21 22 12 C2 12 12 0.54000 1 8 13 14 15 16 17 18 19 20 13 N2 7 14 -0.83000 0 5 14 15 16 17 18 14 H21 21 1 0.41500 0 1 15 15 H22 21 1 0.41500 1 0 16 N1 9 14 -0.31000 0 5 17 18 19 20 21 17 H1 21 1 0.31000 1 3 18 19 20 18 C6 12 12 0.45000 0 4 19 20 21 22 19 O6 1 16 -0.45000 1 2 20 21 20 C5 12 12 0.00000 0 3 21 22 23 21 N7 9 14 -0.54000 0 2 22 23 22 C8 12 12 0.44000 0 1 23 23 H8 20 1 0.10000 1 0 24 C2* 14 3 0.15000 0 4 25 26 27 28 25 O2* 3 16 -0.54800 0 2 26 27 26 H2* 21 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 27 C3* 14 3 0.00000 1 28 O3* 3 16 -0.36000 0 # bonds # NB 31 # IB JB MCB 1 2 24 1 3 24 1 4 28 4 5 20 5 6 26 6 7 20 6 27 26 7 8 20 8 9 22 8 24 26 9 10 10 9 22 10 10 11 12 10 20 16 11 12 12 12 13 9 12 16 17 13 14 2 13 15 2 16 17 2 16 18 17 18 19 5 18 20 16 20 21 10 21 22 10 22 23 3 24 25 20 24 27 26 25 26 1 27 28 20 28 29 28 # bond angles # NBA 49 # IB JB KB MCB 0 1 2 14 0 1 3 14 0 1 4 5 2 1 3 29 2 1 4 14 3 1 4 14 1 4 5 26 4 5 6 9 5 6 7 9 5 6 27 8 7 6 27 9 6 7 8 10 7 8 9 9 7 8 24 9 9 8 24 9 8 9 10 37 8 9 22 37 10 9 22 7 9 10 11 39 9 10 20 7 11 10 20 27 10 11 12 27 11 12 13 27 11 12 16 27 13 12 16 27 12 13 14 23 12 13 15 23 14 13 15 24 12 16 17 25 12 16 18 27 17 16 18 25 16 18 19 27 16 18 20 27 19 18 20 27 10 20 18 27 10 20 21 7 18 20 21 39 20 21 22 7 9 22 21 7 9 22 23 36 21 22 23 36 8 24 25 9 8 24 27 8 25 24 27 9 24 25 26 12 6 27 24 8 6 27 28 9 24 27 28 9 27 28 29 26 # improper dihedrals # NIDA 23 # IB JB KB LB MCB 8 10 22 9 1 9 10 20 21 1 10 9 11 20 1 10 9 22 21 1 10 11 12 16 1 10 20 21 22 1 11 10 20 18 1 11 12 16 18 1 12 16 18 20 1 13 11 16 12 1 13 14 15 12 1 16 18 20 10 1 17 12 18 16 1 19 16 20 18 1 20 10 11 12 1 20 18 21 10 1 20 21 22 9 1 22 9 10 20 1 22 9 21 23 1 24 7 9 8 2 24 25 27 8 2 27 5 7 6 2 27 24 28 6 2 # dihedrals # NDA 28 # IB JB KB LB MCB -1 0 1 4 20 -1 0 1 4 27 0 1 4 5 20 0 1 4 5 27 1 4 5 6 7 1 4 5 6 22 4 5 6 7 8 4 5 6 7 25 4 5 6 27 17 4 5 6 27 34 27 6 7 8 29 5 6 27 24 34 5 6 27 28 17 7 6 27 24 17 7 6 27 28 18 6 7 8 24 29 7 8 9 10 16 7 8 24 25 18 7 8 24 27 17 7 8 24 27 34 9 8 24 25 17 11 12 13 14 14 8 24 25 26 23 8 24 27 6 34 8 24 27 28 17 25 24 27 6 17 25 24 27 28 18 6 27 28 29 29 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK CYT SOL TYPE RNUC NAME cytidine 5-phosphoric acid (RNA, charge -e) # building block (residue, nucleotide, etc.) # RNME CYT # number of atoms, number of preceding exclusions # NMAT NLIN 25 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 30 31 0.99000 0 4 2 3 4 5 2 O1P 2 16 -0.63500 0 2 3 4 3 O2P 2 16 -0.63500 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 15 4 0.00000 1 3 6 7 24 6 C4* 14 3 0.16000 0 5 7 8 21 24 25 7 O4* 3 16 -0.36000 0 4 8 9 21 24 8 C1* 14 3 0.20000 1 10 9 10 11 12 13 14 19 21 22 24 9 N1 9 14 -0.20000 0 9 10 11 12 13 14 15 19 20 21 10 C6 12 12 0.10000 0 8 11 12 13 14 15 16 19 20 11 H6 20 1 0.10000 1 4 12 15 19 20 12 C2 12 12 0.45000 0 5 13 14 15 16 19 13 O2 1 16 -0.45000 1 2 14 15 14 N3 9 14 -0.54000 0 4 15 16 19 20 15 C4 12 12 0.54000 1 5 16 17 18 19 20 16 N4 7 14 -0.83000 0 4 17 18 19 20 17 H41 21 1 0.41500 0 1 18 18 H42 21 1 0.41500 1 0 19 C5 12 12 -0.10000 0 1 20 20 H5 20 1 0.10000 1 0 21 C2* 14 3 0.15000 0 4 22 23 24 25 22 O2* 3 16 -0.54800 0 2 23 24 23 H2* 21 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 24 C3* 14 3 0.00000 1 25 O3* 3 16 -0.36000 0 # bonds # NB 27 # IB JB MCB 1 2 24 1 3 24 1 4 28 4 5 20 5 6 26 6 7 20 6 24 26 7 8 20 8 9 23 8 21 26 9 10 17 9 12 17 10 11 3 10 19 16 12 13 5 12 14 12 14 15 12 15 16 9 15 19 16 16 17 2 16 18 2 19 20 3 21 22 20 21 24 26 22 23 1 24 25 20 25 26 28 # bond angles # NBA 42 # IB JB KB MCB 0 1 2 14 0 1 3 14 0 1 4 5 2 1 3 29 2 1 4 14 3 1 4 14 1 4 5 26 4 5 6 9 5 6 7 9 5 6 24 8 7 6 24 9 6 7 8 10 7 8 9 9 7 8 21 9 9 8 21 8 8 9 10 27 8 9 12 27 10 9 12 27 9 10 11 25 9 10 19 27 11 10 19 25 9 12 13 27 9 12 14 27 13 12 14 27 12 14 15 27 14 15 16 27 14 15 19 27 16 15 19 27 15 16 17 23 15 16 18 23 17 16 18 24 10 19 15 27 10 19 20 25 15 19 20 25 8 21 22 9 8 21 24 8 22 21 24 9 21 22 23 12 6 24 21 8 6 24 25 9 21 24 25 9 24 25 26 26 # improper dihedrals # NIDA 16 # IB JB KB LB MCB 9 10 12 8 1 9 10 19 15 1 9 12 14 15 1 10 9 12 14 1 10 9 19 11 1 12 9 10 19 1 12 14 15 19 1 13 9 14 12 1 14 15 19 10 1 16 14 19 15 1 16 17 18 15 1 19 10 15 20 1 21 7 9 8 2 21 22 24 8 2 24 5 7 6 2 24 21 25 6 2 # dihedrals # NDA 28 # IB JB KB LB MCB -1 0 1 4 20 -1 0 1 4 27 0 1 4 5 20 0 1 4 5 27 1 4 5 6 7 1 4 5 6 22 4 5 6 7 8 4 5 6 7 25 4 5 6 24 17 4 5 6 24 34 24 6 7 8 29 5 6 24 21 34 5 6 24 25 17 7 6 24 21 17 7 6 24 25 18 6 7 8 21 29 7 8 9 12 16 7 8 21 22 18 7 8 21 24 17 7 8 21 24 34 9 8 21 22 17 14 15 16 17 14 8 21 22 23 23 8 21 24 6 34 8 21 24 25 17 22 21 24 6 17 22 21 24 25 18 6 24 25 26 29 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK URA SOL TYPE RNUC NAME uridine 5-phosphoric acid (RNA, charge -e) # building block (residue, nucleotide, etc.) # RNME URA # number of atoms, number of preceding exclusions # NMAT NLIN 24 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 30 31 0.99000 0 4 2 3 4 5 2 O1P 2 16 -0.63500 0 2 3 4 3 O2P 2 16 -0.63500 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 15 4 0.00000 1 3 6 7 23 6 C4* 14 3 0.16000 0 5 7 8 20 23 24 7 O4* 3 16 -0.36000 0 4 8 9 20 23 8 C1* 14 3 0.20000 1 10 9 10 11 12 13 14 18 20 21 23 9 N1 9 14 -0.20000 0 10 10 11 12 13 14 15 16 18 19 20 10 C6 12 12 0.10000 0 8 11 12 13 14 16 17 18 19 11 H6 20 1 0.10000 1 4 12 16 18 19 12 C2 12 12 0.45000 0 6 13 14 15 16 17 18 13 O2 1 16 -0.45000 1 3 14 15 16 14 N3 9 14 -0.31000 0 5 15 16 17 18 19 15 H3 21 1 0.31000 1 3 16 17 18 16 C4 12 12 0.45000 0 3 17 18 19 17 O4 1 16 -0.45000 1 2 18 19 18 C5 12 12 -0.10000 0 1 19 19 H5 20 1 0.10000 1 0 20 C2* 14 3 0.15000 0 4 21 22 23 24 21 O2* 3 16 -0.54800 0 2 22 23 22 H2* 21 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 23 C3* 14 3 0.00000 1 24 O3* 3 16 -0.36000 0 # bonds # NB 26 # IB JB MCB 1 2 24 1 3 24 1 4 28 4 5 20 5 6 26 6 7 20 6 23 26 7 8 20 8 9 23 8 20 26 9 10 17 9 12 17 10 11 3 10 18 16 12 13 5 12 14 17 14 15 2 14 16 17 16 17 5 16 18 16 18 19 3 20 21 20 20 23 26 21 22 1 23 24 20 24 25 28 # bond angles # NBA 41 # IB JB KB MCB 0 1 2 14 0 1 3 14 0 1 4 5 2 1 3 29 2 1 4 14 3 1 4 14 1 4 5 26 4 5 6 9 5 6 7 9 5 6 23 8 7 6 23 9 6 7 8 10 7 8 9 9 7 8 20 9 9 8 20 8 8 9 10 27 8 9 12 27 10 9 12 27 9 10 11 25 9 10 18 27 11 10 18 25 9 12 13 27 9 12 14 27 13 12 14 27 12 14 15 25 12 14 16 27 15 14 16 25 14 16 17 27 14 16 18 27 17 16 18 27 10 18 16 27 10 18 19 25 16 18 19 25 8 20 21 9 8 20 23 8 21 20 23 9 20 21 22 12 6 23 20 8 6 23 24 9 20 23 24 9 23 24 25 26 # improper dihedrals # NIDA 16 # IB JB KB LB MCB 9 10 12 8 1 9 10 18 16 1 9 12 14 16 1 10 9 12 14 1 10 9 18 11 1 12 9 10 18 1 12 14 16 18 1 13 9 14 12 1 14 16 18 10 1 15 12 16 14 1 17 14 18 16 1 18 10 16 19 1 20 7 9 8 2 20 21 23 8 2 23 5 7 6 2 23 20 24 6 2 # dihedrals # NDA 27 # IB JB KB LB MCB -1 0 1 4 20 -1 0 1 4 27 0 1 4 5 20 0 1 4 5 27 1 4 5 6 7 1 4 5 6 22 4 5 6 7 8 4 5 6 7 25 4 5 6 23 17 4 5 6 23 34 23 6 7 8 29 5 6 23 20 34 5 6 23 24 17 7 6 23 20 17 7 6 23 24 18 6 7 8 20 29 7 8 9 12 16 7 8 20 21 18 7 8 20 23 17 7 8 20 23 34 9 8 20 21 17 8 20 21 22 23 8 20 23 6 34 8 20 23 24 17 21 20 23 6 17 21 20 23 24 18 6 23 24 25 29 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK DPPC SOL TYPE MOLE NAME dipalmitoylphosphatidylcholine # building block (residue, nucleotide, etc.) # RNME DPPC # number of atoms, number of preceding exclusions # NMAT NLIN 50 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C33 54 5 0.40000 0 4 2 3 4 5 2 C34 54 5 0.40000 0 3 3 4 5 3 C35 54 5 0.40000 0 2 4 5 4 N 8 14 -0.50000 0 2 5 6 5 C32 15 4 0.30000 1 2 6 7 6 C31 15 4 0.40000 0 2 7 8 7 O32 3 16 -0.80000 0 4 8 9 10 11 8 P 30 31 1.70000 0 4 9 10 11 12 9 O33 2 16 -0.80000 0 2 10 11 10 O34 2 16 -0.80000 0 1 11 11 O31 3 16 -0.70000 1 2 12 13 12 C3 15 4 0.40000 0 3 13 14 32 13 C2 14 3 0.30000 0 4 14 15 32 33 14 O21 4 16 -0.70000 0 4 15 16 17 32 15 C21 12 12 0.70000 0 3 16 17 18 16 O22 1 16 -0.70000 1 1 17 17 C22 15 4 0.00000 1 2 18 19 18 C23 15 4 0.00000 1 2 19 20 19 C24 15 4 0.00000 1 2 20 21 20 C25 15 4 0.00000 1 2 21 22 21 C26 15 4 0.00000 1 2 22 23 22 C27 15 4 0.00000 1 2 23 24 23 C28 15 4 0.00000 1 2 24 25 24 C29 15 4 0.00000 1 2 25 26 25 C210 15 4 0.00000 1 2 26 27 26 C211 15 4 0.00000 1 2 27 28 27 C212 15 4 0.00000 1 2 28 29 28 C213 15 4 0.00000 1 2 29 30 29 C214 15 4 0.00000 1 2 30 31 30 C215 15 4 0.00000 1 1 31 31 C216 16 5 0.00000 1 0 32 C1 15 4 0.50000 0 2 33 34 33 O11 4 16 -0.70000 0 3 34 35 36 34 C11 12 12 0.80000 0 3 35 36 37 35 O12 1 16 -0.60000 1 1 36 36 C12 15 4 0.00000 1 2 37 38 37 C13 15 4 0.00000 1 2 38 39 38 C14 15 4 0.00000 1 2 39 40 39 C15 15 4 0.00000 1 2 40 41 40 C16 15 4 0.00000 1 2 41 42 41 C17 15 4 0.00000 1 2 42 43 42 C18 15 4 0.00000 1 2 43 44 43 C19 15 4 0.00000 1 2 44 45 44 C110 15 4 0.00000 1 2 45 46 45 C111 15 4 0.00000 1 2 46 47 46 C112 15 4 0.00000 1 2 47 48 47 C113 15 4 0.00000 1 2 48 49 48 C114 15 4 0.00000 1 2 49 50 49 C115 15 4 0.00000 1 1 50 50 C116 16 5 0.00000 1 0 # bonds # NB 49 # IB JB MCB 1 4 21 2 4 21 3 4 21 4 5 21 5 6 27 6 7 18 7 8 28 8 9 24 8 10 24 8 11 28 11 12 18 12 13 27 13 14 18 13 32 27 14 15 10 15 16 5 15 17 23 17 18 27 18 19 27 19 20 27 20 21 27 21 22 27 22 23 27 23 24 27 24 25 27 25 26 27 26 27 27 27 28 27 28 29 27 29 30 27 30 31 27 32 33 18 33 34 10 34 35 5 34 36 23 36 37 27 37 38 27 38 39 27 39 40 27 40 41 27 41 42 27 42 43 27 43 44 27 44 45 27 45 46 27 46 47 27 47 48 27 48 49 27 49 50 27 # bond angles # NBA 57 # IB JB KB MCB 1 4 2 13 1 4 3 13 1 4 5 13 2 4 3 13 2 4 5 13 3 4 5 13 4 5 6 15 5 6 7 15 6 7 8 26 7 8 9 14 7 8 10 14 7 8 11 5 9 8 10 29 9 8 11 14 10 8 11 14 8 11 12 26 11 12 13 15 12 13 14 13 12 13 32 13 14 13 32 13 13 14 15 22 14 15 16 31 14 15 17 16 16 15 17 35 15 17 18 15 17 18 19 15 18 19 20 15 19 20 21 15 20 21 22 15 21 22 23 15 22 23 24 15 23 24 25 15 24 25 26 15 25 26 27 15 26 27 28 15 27 28 29 15 28 29 30 15 29 30 31 15 13 32 33 15 32 33 34 22 33 34 35 31 33 34 36 16 35 34 36 35 34 36 37 15 36 37 38 15 37 38 39 15 38 39 40 15 39 40 41 15 40 41 42 15 41 42 43 15 42 43 44 15 43 44 45 15 44 45 46 15 45 46 47 15 46 47 48 15 47 48 49 15 48 49 50 15 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 14 12 32 13 2 15 14 17 16 1 34 33 36 35 1 # dihedrals # NDA 43 # IB JB KB LB MCB 1 4 5 6 29 4 5 6 7 4 4 5 6 7 36 5 6 7 8 29 6 7 8 11 20 6 7 8 11 27 7 8 11 12 20 7 8 11 12 27 8 11 12 13 29 11 12 13 32 34 12 13 14 15 29 12 13 32 33 34 13 14 15 17 13 14 15 17 18 40 15 17 18 19 34 17 18 19 20 34 18 19 20 21 34 19 20 21 22 34 20 21 22 23 34 21 22 23 24 34 22 23 24 25 34 23 24 25 26 34 24 25 26 27 34 25 26 27 28 34 26 27 28 29 34 27 28 29 30 34 28 29 30 31 34 13 32 33 34 29 32 33 34 36 13 33 34 36 37 40 34 36 37 38 34 36 37 38 39 34 37 38 39 40 34 38 39 40 41 34 39 40 41 42 34 40 41 42 43 34 41 42 43 44 34 42 43 44 45 34 43 44 45 46 34 44 45 46 47 34 45 46 47 48 34 46 47 48 49 34 47 48 49 50 34 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK CH4 SOL TYPE MOLE NAME methane (united atom) # building block (residue, nucleotide, etc.) # RNME CH4 # number of atoms, number of preceding exclusions # NMAT NLIN 1 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 CM 17 6 0.00000 1 0 # bonds # NB 0 # IB JB MCB # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK AR SOL TYPE MOLE NAME argon # building block (residue, nucleotide, etc.) # RNME AR # number of atoms, number of preceding exclusions # NMAT NLIN 1 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 AR 31 39 0.00000 1 0 # bonds # NB 0 # IB JB MCB # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK SO42- SOL TYPE MOLE NAME SO_4^-- ion (charge -2e) # building block (residue, nucleotide, etc.) # RNME SO42- # 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 IS 23 32 0.54000 0 4 2 3 4 5 2 IO1 2 16 -0.63500 0 3 3 4 5 3 IO2 2 16 -0.63500 0 2 4 5 4 IO3 2 16 -0.63500 0 1 5 5 IO4 2 16 -0.63500 1 0 # bonds # NB 4 # IB JB MCB 1 2 25 1 3 25 1 4 25 1 5 25 # bond angles # NBA 6 # IB JB KB MCB 2 1 3 13 2 1 4 13 2 1 5 13 3 1 4 13 3 1 5 13 4 1 5 13 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK ZN2+ SOL TYPE MOLE NAME zinc ion (charge +2e) # building block (residue, nucleotide, etc.) # RNME ZN2+ # number of atoms, number of preceding exclusions # NMAT NLIN 1 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 ZN 27 65 2.00000 1 0 # bonds # NB 0 # IB JB MCB # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK NA+ SOL TYPE MOLE NAME sodium ion (charge +e) # building block (residue, nucleotide, etc.) # RNME NA+ # number of atoms, number of preceding exclusions # NMAT NLIN 1 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 NA 37 23 1.00000 1 0 # bonds # NB 0 # IB JB MCB # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK CL- SOL TYPE MOLE NAME chlorine ion (charge -e) # building block (residue, nucleotide, etc.) # RNME CL- # number of atoms, number of preceding exclusions # NMAT NLIN 1 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 CL 38 35 -1.00000 1 0 # bonds # NB 0 # IB JB MCB # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK CA2+ SOL TYPE MOLE NAME calcium ion (charge +2e) # building block (residue, nucleotide, etc.) # RNME CA2+ # number of atoms, number of preceding exclusions # NMAT NLIN 1 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 CA 29 40 2.00000 1 0 # bonds # NB 0 # IB JB MCB # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK MG2+ SOL TYPE MOLE NAME magnesium ion (charge +2e) # building block (residue, nucleotide, etc.) # RNME MG2+ # number of atoms, number of preceding exclusions # NMAT NLIN 1 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 MG 28 24 2.00000 1 0 # bonds # NB 0 # IB JB MCB # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK CU1+ SOL TYPE MOLE NAME copper ion (charge +e) # building block (residue, nucleotide, etc.) # RNME CU1+ # number of atoms, number of preceding exclusions # NMAT NLIN 1 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 CU 24 63 1.00000 1 0 # bonds # NB 0 # IB JB MCB # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK CU2+ SOL TYPE MOLE NAME copper ion (charge +2e) # building block (residue, nucleotide, etc.) # RNME CU2+ # number of atoms, number of preceding exclusions # NMAT NLIN 1 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 CU 25 63 2.00000 1 0 # bonds # NB 0 # IB JB MCB # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK H2O SOL TYPE MOLE NAME water (SPC model) # building block (residue, nucleotide, etc.) # RNME H2O # 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 OW 5 16 -0.82000 0 2 2 3 2 HW1 21 1 0.41000 0 1 3 3 HW2 21 1 0.41000 1 0 # bonds # NB 3 # IB JB MCB 1 2 38 1 3 38 2 3 46 # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK H2OE SOL TYPE MOLE NAME water (SPC-E model) # building block (residue, nucleotide, etc.) # RNME H2OE # 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 OW 5 16 -0.84760 0 2 2 3 2 HW1 21 1 0.42380 0 1 3 3 HW2 21 1 0.42380 1 0 # bonds # NB 3 # IB JB MCB 1 2 38 1 3 38 2 3 46 # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK CHCL3 SOL TYPE MOLE NAME chloroform # building block (residue, nucleotide, etc.) # RNME CHCL3 # 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 CChl 39 12 0.17900 0 4 2 3 4 5 2 HChl 41 1 0.08200 0 3 3 4 5 3 CLCh1 40 35 -0.08700 0 2 4 5 4 CLCh2 40 35 -0.08700 0 1 5 5 CLCh3 40 35 -0.08700 1 0 # bonds # NB 9 # IB JB MCB 1 3 40 1 4 40 1 5 40 2 3 47 2 4 47 2 5 47 3 4 48 3 5 48 4 5 48 # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK DMSO SOL TYPE MOLE NAME dimethylsulfoxide # building block (residue, nucleotide, etc.) # RNME DMSO # 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 SDmso 42 32 0.12753 0 3 2 3 4 2 ODmso 44 16 -0.44753 0 2 3 4 3 CDms1 43 5 0.16000 0 1 4 4 CDms2 43 5 0.16000 1 0 # bonds # NB 6 # IB JB MCB 1 2 41 1 3 42 1 4 42 2 3 49 2 4 49 3 4 50 # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK CH3OH SOL TYPE MOLE NAME methanol # building block (residue, nucleotide, etc.) # RNME CH3OH # 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 Omet 36 16 -0.67400 0 2 2 3 2 HMet 21 1 0.40800 0 1 3 3 CMet 35 5 0.26600 1 0 # bonds # NB 3 # IB JB MCB 1 2 1 1 3 27 2 3 51 # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK CCL4 SOL TYPE MOLE NAME carbontetrachloride # building block (residue, nucleotide, etc.) # RNME CCL4 # 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 CCl4 45 12 0.00000 0 4 2 3 4 5 2 CLCl1 46 35 0.00000 0 3 3 4 5 3 CLCl2 46 35 0.00000 0 2 4 5 4 CLCl3 46 35 0.00000 0 1 5 5 CLCl4 46 35 0.00000 1 0 # bonds # NB 9 # IB JB MCB 1 2 43 1 3 43 1 4 43 1 5 43 2 3 52 2 4 52 2 5 52 3 4 52 3 5 52 # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK TFE SOL TYPE MOLE NAME 2,2,2-trifluoroethanol # building block (residue, nucleotide, etc.) # RNME TFE # 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 HT 21 1 0.41000 0 2 2 3 2 OT 50 16 -0.62500 0 2 3 4 3 CH2T 49 4 0.27300 0 4 4 5 6 7 4 CT 48 12 0.45200 0 3 5 6 7 5 F1T 47 19 -0.17000 0 2 6 7 6 F2T 47 19 -0.17000 0 1 7 7 F3T 47 19 -0.17000 1 0 # bonds # NB 6 # IB JB MCB 1 2 1 2 3 18 3 4 27 4 5 13 4 6 13 4 7 13 # bond angles # NBA 8 # IB JB KB MCB 1 2 3 50 2 3 4 51 3 4 5 52 3 4 6 52 3 4 7 52 5 4 6 49 5 4 7 49 6 4 7 49 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 1 2 3 4 24 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8.mtb BLK UREA SOL TYPE MOLE NAME urea # building block (residue, nucleotide, etc.) # RNME UREA # 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 OU 52 16 -0.39000 0 7 2 3 4 5 6 7 8 2 CU 51 12 0.14200 0 6 3 4 5 6 7 8 3 N1U 53 14 -0.54200 0 5 4 5 6 7 8 4 H11U 21 1 0.33300 0 4 5 6 7 8 5 H12U 21 1 0.33300 0 3 6 7 8 6 N2U 53 14 -0.54200 0 2 7 8 7 H21U 21 1 0.33300 0 1 8 8 H22U 21 1 0.33300 1 0 # bonds # NB 7 # IB JB MCB 1 2 44 2 3 45 2 6 45 3 4 2 3 5 2 6 7 2 6 8 2 # bond angles # NBA 9 # IB JB KB MCB 1 2 3 54 1 2 6 54 3 2 6 53 2 3 4 23 2 3 5 23 4 3 5 24 2 6 7 23 2 6 8 23 7 6 8 24 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 2 3 6 1 1 3 4 5 2 1 6 7 8 2 1 # dihedrals # NDA 2 # IB JB KB LB MCB 1 2 3 4 15 1 2 6 7 15 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLVENT #@BLOCKTYPE 54a8.mtb BLK H2O SVT TYPE MOLE NAME water (SPC model) #solvent name #RNMES H2O #number of atoms 3 #atoms #ATOM ANM IAC MASS CG 1 OW 5 16 -.82 2 HW1 21 1 .41 3 HW2 21 1 .41 #constraints #number 3 # IB JB LENGTH 1 2 0.1 1 3 0.1 2 3 0.163299 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE 54a8.mtb BLK H2OE SVT TYPE MOLE NAME water (SPC-E model) #solvent name #RNMES H2OE #number of atoms 3 #atoms #ATOM ANM IAC MASS CG 1 OW 5 16 -.8476 2 HW1 21 1 .4238 3 HW2 21 1 .4238 #constraints #number 3 # IB JB LENGTH 1 2 0.1 1 3 0.1 2 3 0.163299 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE 54a8.mtb BLK CHCL3 SVT TYPE MOLE NAME chloroform #solvent name #RNMES CHCL3 #number of atoms 5 #atoms #ATOM ANM IAC MASS CG 1 CChl 39 12 .179 2 HChl 41 1 .082 3 CLCh1 40 35 -.087 4 CLCh2 40 35 -.087 5 CLCh3 40 35 -.087 #constraints #number 9 # IB JB LENGTH 1 3 0.1758 1 4 0.1758 1 5 0.1758 2 3 0.233839 2 4 0.233839 2 5 0.233839 3 4 0.290283 3 5 0.290283 4 5 0.290283 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE 54a8.mtb BLK DMSO SVT TYPE MOLE NAME dimethylsulfoxide #solvent name #RNMES DMSO #number of atoms 4 #atoms #ATOM ANM IAC MASS CG 1 SDmso 42 32 .12753 2 ODmso 44 16 -.44753 3 CDms1 43 5 .16 4 CDms2 43 5 .16 #constraints #number 6 # IB JB LENGTH 1 2 0.153 1 3 0.1937991 1 4 0.1937991 2 3 0.2793883 2 4 0.2793883 3 4 0.2911886 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE 54a8.mtb BLK CH3OH SVT TYPE MOLE NAME methanol #solvent name #RNMES CH3OH #number of atoms 3 #atoms #ATOM ANM IAC MASS CG 1 OMet 36 16 -.674 2 HMet 21 1 .408 3 CMet 35 5 .266 #constraints #number 3 # IB JB LENGTH 1 2 0.1000 1 3 0.1530 2 3 0.2077 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE 54a8.mtb BLK CCL4 SVT TYPE MOLE NAME carbontetrachloride #solvent name #RNMES CCL4 #number of atoms 5 #atoms #ATOM ANM IAC MASS CG 1 CCl4 45 12 .0 2 CLCl1 46 35 .0 3 CLCl2 46 35 .0 4 CLCl3 46 35 .0 5 CLCl4 46 35 .0 #constraints #number 9 # IB JB LENGTH 1 2 0.176 1 3 0.176 1 4 0.176 1 5 0.176 2 3 0.287407 2 4 0.287407 2 5 0.287407 3 4 0.287407 3 5 0.287407 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 54a8.mtb BLK NH3+ INI TYPE APEP NAME N-terminal peptide end-group (protonated, charge +e) # building block (residue, nucleotide, etc.) # RNME NH3+ # number of atoms, number of atoms to be replaced # NMAT NREP 5 3 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE # Change 54A7->54A8 --- new charges for atoms 1-5 1 H1 21 1 0.25000 0 4 2 3 4 5 2 H2 21 1 0.25000 0 3 3 4 5 # replacing atoms 3 N 8 14 0.05000 0 4 H3 21 1 0.25000 0 5 CA 14 3 0.20000 1 # bonds # NB 2 # IB JB MCB 1 3 2 2 3 2 # bond angles # NBA 6 # IB JB KB MCB 1 3 2 10 1 3 4 10 1 3 5 11 2 3 4 10 2 3 5 11 4 3 5 11 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 2 3 5 6 29 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE 54a8.mtb BLK NH2 INI TYPE APEP NAME N-terminal peptide end-group (deprotonated, neutral) # building block (residue, nucleotide, etc.) # RNME NH2 # number of atoms, number of atoms to be replaced # NMAT NREP 4 3 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H1 21 1 0.44000 0 3 2 3 4 # replacing atoms 2 N 7 14 -0.64000 0 3 H2 21 1 0.44000 0 4 CA 14 3 -0.24000 1 # bonds # NB 1 # IB JB MCB 1 2 2 # bond angles # NBA 3 # IB JB KB MCB 1 2 3 10 1 2 4 11 3 2 4 11 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 1 2 4 5 29 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE 54a8.mtb BLK NPRO INI TYPE APEP NAME N-terminal peptide end-group for proline or hydroxy proline (protonated, charge +e) # building block (residue, nucleotide, etc.) # RNME NPRO # number of atoms, number of atoms to be replaced # NMAT NREP 7 5 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE # Change 54A7->54A8 --- new charges for atoms 1-4 1 H1 21 1 0.25000 0 4 2 3 4 7 2 H2 21 1 0.25000 0 3 3 4 7 # replacing atoms 3 N 8 14 0.10000 0 4 CA 14 3 0.20000 0 5 CB 15 4 0.00000 0 6 CG 15 4 0.00000 0 # Change 54A7->54A8 --- new charges for atom 7 7 CD 15 4 0.20000 1 # bonds # NB 7 # IB JB MCB 1 3 2 2 3 2 3 4 21 3 7 21 4 5 27 5 6 27 6 7 27 # bond angles # NBA 10 # IB JB KB MCB 1 3 2 10 1 3 4 11 1 3 7 11 2 3 4 11 2 3 7 11 4 3 7 21 3 4 5 13 4 5 6 13 5 6 7 13 3 7 6 13 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 2 3 4 8 29 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE 54a8.mtb BLK COO- TER TYPE APEP NAME C-terminal peptide end-group (deprotonated, charge -e) # building block (residue, nucleotide, etc.) # RNME COO- # number of atoms, number of atoms to be replaced # NMAT NREP # Change 54A7->54A8 --- CA is now included (with modified charge), so ( 3 -2 ) -> ( 4 -3 ) 4 -3 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE # Change 54A7->54A8 --- new charges for atoms 1-4 (previously we only had 1-3) # negative IAC now recognized by make_top (May 2012) as # meaning "the closest preceding atom with the indicated name" 1 CA -1 3 0.16000 1 0 2 C 12 12 0.27000 0 2 3 4 3 O1 2 16 -0.71500 0 1 4 4 O2 2 16 -0.71500 1 0 # bonds # NB 2 # IB JB MCB # Change 54A7->54A8 --- numbering adjusted 2 3 6 2 4 6 # bond angles # NBA 3 # IB JB KB MCB # Change 54A7->54A8 --- numbering adjusted 1 2 3 22 1 2 4 22 3 2 4 38 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE 54a8.mtb BLK COOH TER TYPE APEP NAME C-terminal peptide end-group (protonated, neutral) # building block (residue, nucleotide, etc.) # RNME COOH # number of atoms, number of atoms to be replaced # NMAT NREP 4 -2 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C 12 12 0.33000 0 3 2 3 4 2 O1 1 16 -0.45000 0 1 3 3 O2 3 16 -0.28800 0 1 4 4 H 21 1 0.40800 1 0 # bonds # NB 3 # IB JB MCB 1 2 5 1 3 13 3 4 1 # bond angles # NBA 1 # IB JB KB MCB 1 3 4 12 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 0 1 3 4 12 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE 54a8.mtb BLK D5OH INI TYPE DNUC NAME 5-terminal DNA end-group # building block (residue, nucleotide, etc.) # RNME D5OH # number of atoms, number of atoms to be replaced # NMAT NREP 5 5 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE # replacing atoms 1 H5* 21 1 0.39800 0 2 O1P 0 1 0.00000 0 3 O2P 0 1 0.00000 0 4 O5* 3 16 -0.54800 0 5 C5* 15 4 0.15000 1 # bonds # NB 2 # IB JB MCB 1 4 1 4 5 20 # bond angles # NBA 1 # IB JB KB MCB 1 4 5 12 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 1 4 5 6 23 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE 54a8.mtb BLK 5OH INI TYPE RNUC NAME 5-terminal RNA end-group # building block (residue, nucleotide, etc.) # RNME 5OH # number of atoms, number of atoms to be replaced # NMAT NREP 5 5 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE # replacing atoms 1 H5* 21 1 0.39800 0 2 O1P 0 1 0.00000 0 3 O2P 0 1 0.00000 0 4 O5* 3 16 -0.54800 0 5 C5* 15 4 0.15000 1 # bonds # NB 2 # IB JB MCB 1 4 1 4 5 20 # bond angles # NBA 1 # IB JB KB MCB 1 4 5 12 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 1 4 5 6 23 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE 54a8.mtb BLK D3OH TER TYPE DNUC NAME 3-terminal DNA end-group # building block (residue, nucleotide, etc.) # RNME D3OH # number of atoms, number of atoms to be replaced # NMAT NREP 4 -3 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C2* 18 4 0.00000 1 2 2 3 2 C3* 14 3 0.15000 0 2 3 4 3 O3* 3 16 -0.54800 0 1 4 4 H3* 21 1 0.39800 1 0 # bonds # NB 2 # IB JB MCB 2 3 20 3 4 1 # bond angles # NBA 1 # IB JB KB MCB 2 3 4 12 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 0 2 3 4 23 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE 54a8.mtb BLK 3OH TER TYPE RNUC NAME 3-terminal RNA end-group # building block (residue, nucleotide, etc.) # RNME 3OH # number of atoms, number of atoms to be replaced # NMAT NREP 6 -5 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C2* 14 3 0.15000 0 4 2 3 4 5 2 O2* 3 16 -0.54800 0 2 3 4 3 H2* 21 1 0.39800 1 0 4 C3* 14 3 0.15000 0 2 5 6 5 O3* 3 16 -0.54800 0 1 6 6 H3* 21 1 0.39800 1 0 # bonds # NB 5 # IB JB MCB 1 2 20 1 4 26 2 3 1 4 5 20 5 6 1 # bond angles # NBA 4 # IB JB KB MCB 2 1 4 9 1 2 3 12 1 4 5 9 4 5 6 12 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 0 4 5 6 29 #@FREELINE # LJ exceptions # NEX 0 END