TITLE File : 43b1.mtb Force field : 43B1 (vacuum simulations) Reference : van Gunsteren et al. Biomolecular Simulation: The GROMOS96 Manual and User Guide, vdf Hochschulverlag AG an der ETH Zuerich and Biomos b.v., Zuerich, Groningen, 1996, pp. 1-1042 File content : molecular topology building blocks (all available building blocks) Format : GROMOS11 Initial file : PHH, Zuerich, May 2011 Time stamp : PHH, Thu Nov 10 22:07:56 CET 2011 Remark : Original force field of the GROMOS96 distribution Remark : DG, NS, Oct 07: exclusion errors corrected in FMNR, ATP, TMP, THF and HEME Remark : DG, CO, Jan 08: errors in improper dihedrals 21-24 in NADH corrected Remark : These two changes become permanent from 53A(B)5 onward Remark : PHH, May 2011 - finalized GROMOS11 file distribution - enforced sequential ordering by (central) atom numbers in covalent terms for all files (no effect on GROMOS11 make_top; make_top enforced it anyway, but now, we avoid the big list of warnings) Modifications : [list below changes after May 2011 - with initials, location and date - and update time stamp] PHH, 09.11.2011: Reintroduced a FORCEFIELD block in all GROMOS11 files. END FORCEFIELD 43B1 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 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE ALA # 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 5 14 -0.28000 0 4 2 3 4 5 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 4 4 5 6 7 4 CB 14 5 0.00000 1 1 5 # trailing atoms #ATOM ANM IACM MASS CGMICGM 5 C 11 12 0.38000 0 6 O 1 16 -0.38000 1 # bonds # NB 6 # IB JB MCB 1 2 2 1 3 20 3 5 26 5 6 4 5 7 9 3 4 26 # bond angles # NBA 9 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 5 12 3 5 7 18 3 5 6 29 6 5 7 32 1 3 4 12 4 3 5 12 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 5 3 7 6 1 3 1 5 4 2 # dihedrals # NDA 3 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 5 19 1 3 5 7 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE ARG # 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 5 14 -0.28000 0 4 2 3 4 16 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 16 17 18 4 CB 13 4 0.00000 0 3 5 6 16 5 CG 13 4 0.00000 1 2 6 7 6 CD 13 4 0.00000 0 3 7 8 9 7 NE 10 14 -0.24000 0 4 8 9 10 13 8 HE 18 1 0.24000 0 1 9 9 CZ 11 12 0.00000 0 6 10 11 12 13 14 15 10 NH1 9 14 -0.48000 0 3 11 12 13 11 HH11 18 1 0.24000 0 1 12 12 HH12 18 1 0.24000 0 0 13 NH2 9 14 -0.48000 0 2 14 15 14 HH21 18 1 0.24000 0 1 15 15 HH22 18 1 0.24000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 16 C 11 12 0.38000 0 17 O 1 16 -0.38000 1 # bonds # NB 17 # IB JB MCB 1 2 2 1 3 20 3 16 26 16 17 4 16 18 9 3 4 26 4 5 26 5 6 26 6 7 20 7 8 2 # 10 7 9 10 9 10 10 9 13 10 10 11 2 10 12 2 13 14 2 13 15 2 # bond angles # NBA 24 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 16 12 3 16 18 18 3 16 17 29 17 16 18 32 1 3 4 12 4 3 16 12 3 4 5 14 # 10 4 5 6 14 5 6 7 12 6 7 8 19 8 7 9 22 6 7 9 32 7 9 10 27 7 9 13 27 10 9 13 27 9 10 11 22 9 10 12 22 # 20 11 10 12 23 9 13 14 22 9 13 15 22 14 13 15 23 # improper dihedrals # NIDA 7 # IB JB KB LB MCB 1 -1 3 2 1 16 3 18 17 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 # dihedrals # NDA 10 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 16 19 1 3 16 18 20 1 3 4 5 17 3 4 5 6 17 4 5 6 7 17 5 6 7 9 19 6 7 9 10 4 7 9 10 11 4 7 9 13 14 4 # 10 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE ARGN # 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 5 14 -0.28000 0 4 2 3 4 15 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 15 16 17 4 CB 13 4 0.00000 1 3 5 6 15 5 CG 13 4 0.00000 0 2 6 7 6 CD 13 4 0.00000 1 3 7 8 9 7 NE 10 14 -0.28000 0 4 8 9 10 12 8 HE 18 1 0.28000 1 1 9 9 CZ 11 12 0.15000 0 5 10 11 12 13 14 10 NH1 10 14 -0.54800 0 2 11 12 11 HH1 18 1 0.39800 1 0 12 NH2 9 14 -0.83000 0 2 13 14 13 HH21 18 1 0.41500 0 1 14 14 HH22 18 1 0.41500 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 15 C 11 12 0.38000 0 16 O 1 16 -0.38000 1 # bonds # NB 16 # IB JB MCB 1 2 2 1 3 20 3 15 26 15 16 4 15 17 9 3 4 26 4 5 26 5 6 26 6 7 20 7 8 2 # 10 7 9 10 9 10 10 9 12 10 10 11 2 12 13 2 12 14 2 # bond angles # NBA 22 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 15 12 3 15 17 18 3 15 16 29 16 15 17 32 1 3 4 12 4 3 15 12 3 4 5 14 # 10 4 5 6 14 5 6 7 12 6 7 8 19 8 7 9 22 6 7 9 32 7 9 10 27 7 9 12 27 10 9 12 27 9 10 11 22 9 12 13 22 # 20 9 12 14 22 13 12 14 23 # improper dihedrals # NIDA 6 # IB JB KB LB MCB 1 -1 3 2 1 15 3 17 16 1 3 1 15 4 2 7 6 9 8 1 9 10 12 7 1 12 13 14 9 1 # dihedrals # NDA 10 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 15 19 1 3 15 17 20 1 3 4 5 17 3 4 5 6 17 4 5 6 7 17 5 6 7 9 19 6 7 9 10 4 7 9 10 11 4 7 9 12 13 4 # 10 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE ASN # 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 5 14 -0.28000 0 4 2 3 4 10 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 10 11 12 4 CB 13 4 0.00000 1 4 5 6 7 10 5 CG 11 12 0.38000 0 4 6 7 8 9 6 OD1 1 16 -0.38000 1 1 7 7 ND2 6 14 -0.83000 0 2 8 9 8 HD21 18 1 0.41500 0 1 9 9 HD22 18 1 0.41500 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 10 C 11 12 0.38000 0 11 O 1 16 -0.38000 1 # bonds # NB 11 # IB JB MCB 1 2 2 1 3 20 3 10 26 10 11 4 10 12 9 3 4 26 4 5 26 5 6 4 5 7 8 7 8 2 # 10 7 9 2 # bond angles # NBA 16 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 10 12 3 10 12 18 3 10 11 29 11 10 12 32 1 3 4 12 4 3 10 12 3 4 5 14 # 10 4 5 6 29 4 5 7 18 6 5 7 32 5 7 8 22 5 7 9 22 8 7 9 23 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 1 -1 3 2 1 10 3 12 11 1 3 1 10 4 2 5 6 7 4 1 7 8 9 5 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 10 19 1 3 10 12 20 1 3 4 5 17 3 4 5 7 20 4 5 7 8 4 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE ASN1 # 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 5 14 -0.28000 0 4 2 3 4 10 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 10 11 12 4 CB 13 4 0.00000 1 4 5 6 7 10 5 CG 11 12 0.38000 0 4 6 7 8 9 6 OD1 1 16 -0.38000 1 1 7 7 ND2 7 14 -0.83000 0 2 8 9 8 HD21 18 1 0.41500 0 1 9 9 HD22 18 1 0.41500 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 10 C 11 12 0.38000 0 11 O 1 16 -0.38000 1 # bonds # NB 11 # IB JB MCB 1 2 2 1 3 20 3 10 26 10 11 4 10 12 9 3 4 26 4 5 26 5 6 4 5 7 8 7 8 2 # 10 7 9 2 # bond angles # NBA 16 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 10 12 3 10 12 18 3 10 11 29 11 10 12 32 1 3 4 12 4 3 10 12 3 4 5 14 # 10 4 5 6 29 4 5 7 18 6 5 7 32 5 7 8 22 5 7 9 22 8 7 9 23 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 1 -1 3 2 1 10 3 12 11 1 3 1 10 4 2 5 6 7 4 1 7 8 9 5 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 10 19 1 3 10 12 20 1 3 4 5 17 3 4 5 7 20 4 5 7 8 4 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE ASP # 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 5 14 -0.28000 0 4 2 3 4 8 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 8 9 10 4 CB 13 4 0.00000 1 4 5 6 7 8 5 CG 11 12 0.72000 0 2 6 7 6 OD1 2 16 -0.36000 0 1 7 7 OD2 2 16 -0.36000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 11 12 0.38000 0 9 O 1 16 -0.38000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 20 3 8 26 8 9 4 8 10 9 3 4 26 4 5 26 5 6 5 5 7 5 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 8 12 3 8 10 18 3 8 9 29 9 8 10 32 1 3 4 12 4 3 8 12 3 4 5 14 # 10 4 5 6 21 4 5 7 21 6 5 7 37 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 8 3 10 9 1 3 1 8 4 2 5 6 7 4 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 8 19 1 3 8 10 20 1 3 4 5 17 3 4 5 6 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE ASPH # 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 5 14 -0.28000 0 4 2 3 4 9 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 9 10 11 4 CB 13 4 0.00000 1 4 5 6 7 9 5 CG 11 12 0.53000 0 3 6 7 8 6 OD1 1 16 -0.38000 0 1 7 7 OD2 3 16 -0.54800 0 1 8 8 HD2 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 9 C 11 12 0.38000 0 10 O 1 16 -0.38000 1 # bonds # NB 10 # IB JB MCB 1 2 2 1 3 20 3 9 26 9 10 4 9 11 9 3 4 26 4 5 26 5 6 4 5 7 12 7 8 1 # 10 # bond angles # NBA 14 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 9 12 3 9 11 18 3 9 10 29 10 9 11 32 1 3 4 12 4 3 9 12 3 4 5 14 # 10 4 5 6 29 4 5 7 18 6 5 7 32 5 7 8 11 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 9 3 11 10 1 3 1 9 4 2 5 6 7 4 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 9 19 1 3 9 11 20 1 3 4 5 17 3 4 5 7 20 4 5 7 8 3 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE CYS # 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 5 14 -0.28000 0 4 2 3 4 6 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 1 5 4 5 6 7 8 4 CB 13 4 0.20000 0 2 5 6 5 SG 20 32 -0.20000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 11 12 0.38000 0 7 O 1 16 -0.38000 1 # bonds # NB 7 # IB JB MCB 1 2 2 1 3 20 3 6 26 6 7 4 6 8 9 3 4 26 4 5 30 # bond angles # NBA 10 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 6 12 3 6 8 18 3 6 7 29 7 6 8 32 1 3 4 12 4 3 6 12 3 4 5 15 # 10 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 6 3 8 7 1 3 1 6 4 2 # dihedrals # NDA 4 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 6 19 1 3 6 8 20 1 3 4 5 17 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE CYSH # 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 5 14 -0.28000 0 4 2 3 4 7 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 7 8 9 4 CB 13 4 0.00000 1 3 5 6 7 5 SG 20 32 -0.06400 0 1 6 6 HG 18 1 0.06400 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 7 C 11 12 0.38000 0 8 O 1 16 -0.38000 1 # bonds # NB 8 # IB JB MCB 1 2 2 1 3 20 3 7 26 7 8 4 7 9 9 3 4 26 4 5 30 5 6 7 # bond angles # NBA 11 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 7 12 3 7 9 18 3 7 8 29 8 7 9 32 1 3 4 12 4 3 7 12 3 4 5 15 # 10 4 5 6 2 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 7 3 9 8 1 3 1 7 4 2 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 7 19 1 3 7 9 20 1 3 4 5 17 3 4 5 6 13 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE CYS1 # 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 5 14 -0.28000 0 4 2 3 4 6 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 6 7 8 4 CB 13 4 0.00000 0 3 5 6 -5 5 SG 20 32 0.00000 1 2 -4 -5 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 11 12 0.38000 0 7 O 1 16 -0.38000 1 # bonds # NB 8 # IB JB MCB 1 2 2 1 3 20 3 6 26 6 7 4 6 8 9 3 4 26 4 5 30 -5 5 33 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 6 12 3 6 8 18 3 6 7 29 7 6 8 32 1 3 4 12 4 3 6 12 3 4 5 15 # 10 -5 5 4 5 -4 -5 5 5 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 6 3 8 7 1 3 1 6 4 2 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 6 19 1 3 6 8 20 1 3 4 5 17 3 4 5 -5 13 -4 -5 5 4 10 5 -5 -4 -3 13 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE CYS2 # 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 5 14 -0.28000 0 4 2 3 4 6 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 6 7 8 4 CB 13 4 0.00000 0 2 5 6 5 SG 20 32 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 11 12 0.38000 0 7 O 1 16 -0.38000 1 # bonds # NB 7 # IB JB MCB 1 2 2 1 3 20 3 6 26 6 7 4 6 8 9 3 4 26 4 5 30 # bond angles # NBA 10 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 6 12 3 6 8 18 3 6 7 29 7 6 8 32 1 3 4 12 4 3 6 12 3 4 5 15 # 10 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 6 3 8 7 1 3 1 6 4 2 # dihedrals # NDA 4 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 6 19 1 3 6 8 20 1 3 4 5 17 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE GLN # 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 5 14 -0.28000 0 4 2 3 4 11 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 11 12 13 4 CB 13 4 0.00000 0 3 5 6 11 5 CG 13 4 0.00000 1 3 6 7 8 6 CD 11 12 0.38000 0 4 7 8 9 10 7 OE1 1 16 -0.38000 1 1 8 8 NE2 6 14 -0.83000 0 2 9 10 9 HE21 18 1 0.41500 0 1 10 10 HE22 18 1 0.41500 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 11 C 11 12 0.38000 0 12 O 1 16 -0.38000 1 # bonds # NB 12 # IB JB MCB 1 2 2 1 3 20 3 11 26 11 12 4 11 13 9 3 4 26 4 5 26 5 6 26 6 7 4 6 8 8 # 10 8 9 2 8 10 2 # bond angles # NBA 17 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 11 12 3 11 13 18 3 11 12 29 12 11 13 32 1 3 4 12 4 3 11 12 3 4 5 14 # 10 4 5 6 14 5 6 7 29 5 6 8 18 7 6 8 32 6 8 9 22 6 8 10 22 9 8 10 23 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 1 -1 3 2 1 11 3 13 12 1 3 1 11 4 2 6 7 8 5 1 8 9 10 6 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 11 19 1 3 11 13 20 1 3 4 5 17 3 4 5 6 17 4 5 6 8 20 5 6 8 9 4 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE GLU # 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 5 14 -0.28000 0 4 2 3 4 9 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 9 10 11 4 CB 13 4 0.00000 0 3 5 6 9 5 CG 13 4 0.00000 1 3 6 7 8 6 CD 11 12 0.72000 0 2 7 8 7 OE1 2 16 -0.36000 0 1 8 8 OE2 2 16 -0.36000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 9 C 11 12 0.38000 0 10 O 1 16 -0.38000 1 # bonds # NB 10 # IB JB MCB 1 2 2 1 3 20 3 9 26 9 10 4 9 11 9 3 4 26 4 5 26 5 6 26 6 7 5 6 8 5 # 10 # bond angles # NBA 14 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 9 12 3 9 11 18 3 9 10 29 10 9 11 32 1 3 4 12 4 3 9 12 3 4 5 14 # 10 4 5 6 14 5 6 7 21 5 6 8 21 7 6 8 37 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 9 3 11 10 1 3 1 9 4 2 6 7 8 5 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 9 19 1 3 9 11 20 1 3 4 5 17 3 4 5 6 17 4 5 6 8 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE GLUH # 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 5 14 -0.28000 0 4 2 3 4 10 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 10 11 12 4 CB 13 4 0.00000 0 3 5 6 10 5 CG 13 4 0.00000 1 3 6 7 8 6 CD 11 12 0.53000 0 3 7 8 9 7 OE1 1 16 -0.38000 0 1 8 8 OE2 3 16 -0.54800 0 1 9 9 HE2 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 10 C 11 12 0.38000 0 11 O 1 16 -0.38000 1 # bonds # NB 11 # IB JB MCB 1 2 2 1 3 20 3 10 26 10 11 4 10 12 9 3 4 26 4 5 26 5 6 26 6 7 4 6 8 12 # 10 8 9 1 # bond angles # NBA 15 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 10 12 3 10 12 18 3 10 11 29 11 10 12 32 1 3 4 12 4 3 10 12 3 4 5 14 # 10 4 5 6 14 5 6 7 29 5 6 8 18 7 6 8 32 6 8 9 11 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 10 3 12 11 1 3 1 10 4 2 6 7 8 5 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 10 19 1 3 10 12 20 1 3 4 5 17 3 4 5 6 17 4 5 6 8 20 5 6 8 9 3 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE GLY # 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 5 14 -0.28000 0 3 2 3 4 2 H 18 1 0.28000 1 1 3 3 CA 13 4 0.00000 1 3 4 5 6 # trailing atoms #ATOM ANM IACM MASS CGMICGM 4 C 11 12 0.38000 0 5 O 1 16 -0.38000 1 # bonds # NB 5 # IB JB MCB 1 2 2 1 3 20 3 4 26 4 5 4 4 6 9 # bond angles # NBA 7 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 4 12 3 4 6 18 3 4 5 29 5 4 6 32 # improper dihedrals # NIDA 2 # IB JB KB LB MCB 1 -1 3 2 1 4 3 6 5 1 # dihedrals # NDA 3 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 4 19 1 3 4 6 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE HISA # building block (residue, nucleotide, etc.) # RNME HISA # 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 5 14 -0.28000 0 4 2 3 4 11 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 11 12 13 4 CB 13 4 0.00000 1 7 5 6 7 8 9 10 11 5 CG 11 12 0.00000 0 5 6 7 8 9 10 6 ND1 8 14 0.00000 0 4 7 8 9 10 7 HD1 18 1 0.19000 0 3 8 9 10 8 CD2 16 3 0.13000 0 2 9 10 9 CE1 16 3 0.26000 0 1 10 10 NE2 8 14 -0.58000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 11 C 11 12 0.38000 0 12 O 1 16 -0.38000 1 # bonds # NB 13 # IB JB MCB 1 2 2 1 3 20 3 11 26 11 12 4 11 13 9 3 4 26 4 5 26 5 6 9 5 8 9 6 7 2 # 10 6 9 9 8 10 9 9 10 9 # bond angles # NBA 19 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 11 12 3 11 13 18 3 11 12 29 12 11 13 32 1 3 4 12 4 3 11 12 3 4 5 14 # 10 4 5 6 36 4 5 8 36 6 5 8 6 5 6 7 35 5 6 9 6 7 6 9 35 5 8 10 6 6 9 10 6 8 10 9 6 # improper dihedrals # NIDA 10 # IB JB KB LB MCB 1 -1 3 2 1 11 3 13 12 1 3 1 11 4 2 5 6 8 4 1 8 5 6 9 1 6 5 8 10 1 5 6 9 10 1 5 8 10 9 1 6 9 10 8 1 6 5 9 7 1 # 10 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 11 19 1 3 11 13 20 1 3 4 5 17 3 4 5 6 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE HISB # building block (residue, nucleotide, etc.) # RNME HISB # 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 5 14 -0.28000 0 4 2 3 4 11 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 11 12 13 4 CB 13 4 0.00000 1 6 5 6 7 8 9 11 5 CG 11 12 0.13000 0 5 6 7 8 9 10 6 ND1 8 14 -0.58000 0 4 7 8 9 10 7 CD2 16 3 0.00000 0 3 8 9 10 8 CE1 16 3 0.26000 0 2 9 10 9 NE2 8 14 0.00000 0 1 10 10 HE2 18 1 0.19000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 11 C 11 12 0.38000 0 12 O 1 16 -0.38000 1 # bonds # NB 13 # IB JB MCB 1 2 2 1 3 20 3 11 26 11 12 4 11 13 9 3 4 26 4 5 26 5 6 9 5 7 9 6 8 9 # 10 7 9 9 8 9 9 9 10 2 # bond angles # NBA 19 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 11 12 3 11 13 18 3 11 12 29 12 11 13 32 1 3 4 12 4 3 11 12 3 4 5 14 # 10 4 5 6 36 4 5 7 36 6 5 7 6 5 6 8 6 5 7 9 6 6 8 9 6 7 9 8 6 7 9 10 35 8 9 10 35 # improper dihedrals # NIDA 10 # IB JB KB LB MCB 1 -1 3 2 1 11 3 13 12 1 3 1 11 4 2 5 6 7 4 1 7 5 6 8 1 6 5 7 9 1 5 6 8 9 1 5 7 9 8 1 6 8 9 7 1 9 7 8 10 1 # 10 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 11 19 1 3 11 13 20 1 3 4 5 17 3 4 5 6 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE HISH # building block (residue, nucleotide, etc.) # RNME HISH # 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 5 14 -0.28000 0 4 2 3 4 12 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 12 13 14 4 CB 13 4 0.00000 1 7 5 6 7 8 9 10 12 5 CG 11 12 0.00000 0 6 6 7 8 9 10 11 6 ND1 8 14 -0.30000 0 5 7 8 9 10 11 7 HD1 18 1 0.30000 0 3 8 9 10 8 CD2 16 3 0.00000 0 3 9 10 11 9 CE1 16 3 0.00000 0 2 10 11 10 NE2 8 14 -0.30000 0 1 11 11 HE2 18 1 0.30000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 12 C 11 12 0.38000 0 13 O 1 16 -0.38000 1 # bonds # NB 14 # IB JB MCB 1 2 2 1 3 20 3 12 26 12 13 4 12 14 9 3 4 26 4 5 26 5 6 9 5 8 9 6 7 2 # 10 6 9 9 8 10 9 9 10 9 10 11 2 # bond angles # NBA 21 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 12 12 3 12 14 18 3 12 13 29 13 12 14 32 1 3 4 12 4 3 12 12 3 4 5 14 # 10 4 5 6 36 4 5 8 36 6 5 8 6 5 6 7 35 5 6 9 6 7 6 9 35 5 8 10 6 6 9 10 6 8 10 9 6 8 10 11 35 # 20 9 10 11 35 # improper dihedrals # NIDA 11 # IB JB KB LB MCB 1 -1 3 2 1 12 3 14 13 1 3 1 12 4 2 5 6 8 4 1 8 5 6 9 1 6 5 8 10 1 5 6 9 10 1 5 8 10 9 1 6 9 10 8 1 6 5 9 7 1 # 10 10 8 9 11 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 12 19 1 3 12 14 20 1 3 4 5 17 3 4 5 6 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE HIS1 # building block (residue, nucleotide, etc.) # RNME HIS1 # 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 5 14 -0.28000 0 4 2 3 4 11 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 11 12 13 4 CB 13 4 0.00000 1 7 5 6 7 8 9 10 11 5 CG 11 12 0.00000 0 6 6 7 8 9 10 -1 6 ND1 8 14 0.00000 0 5 7 8 9 10 -1 7 HD1 18 1 0.19000 0 3 8 9 10 8 CD2 16 3 0.13000 0 3 9 10 -1 9 CE1 16 3 0.26000 0 2 10 -1 10 NE2 8 14 -0.58000 1 5 -1 -2 -3 -4 -5 # trailing atoms #ATOM ANM IACM MASS CGMICGM 11 C 11 12 0.38000 0 12 O 1 16 -0.38000 1 # bonds # NB 14 # IB JB MCB 1 2 2 1 3 20 3 11 26 11 12 4 11 13 9 3 4 26 4 5 26 5 6 9 5 8 9 6 7 2 # 10 6 9 9 8 10 9 9 10 9 -1 10 32 # bond angles # NBA 25 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 11 12 3 11 13 18 3 11 12 29 12 11 13 32 1 3 4 12 4 3 11 12 3 4 5 14 # 10 4 5 6 36 4 5 8 36 6 5 8 6 5 6 7 35 5 6 9 6 7 6 9 35 5 8 10 6 6 9 10 6 8 10 9 6 -1 10 8 33 # 20 -1 10 9 33 -2 -1 10 16 -3 -1 10 16 -4 -1 10 16 -5 -1 10 16 # improper dihedrals # NIDA 10 # IB JB KB LB MCB 1 -1 3 2 1 11 3 13 12 1 3 1 11 4 2 5 6 8 4 1 8 5 6 9 1 6 5 8 10 1 5 6 9 10 1 5 8 10 9 1 6 9 10 8 1 6 5 9 7 1 # 10 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 11 19 1 3 11 13 20 1 3 4 5 17 3 4 5 6 20 -2 -1 10 8 18 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE HYP # 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 5 14 0.00000 1 5 2 3 4 7 8 2 CA 12 3 0.00000 0 6 3 4 7 8 9 10 3 CB 13 4 0.00000 1 4 4 5 7 8 4 CG 12 3 0.15000 0 3 5 6 7 5 OD1 3 16 -0.54800 0 2 6 7 6 HD1 18 1 0.39800 1 0 7 CD2 13 4 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 11 12 0.38000 0 9 O 1 16 -0.38000 1 # bonds # NB 10 # IB JB MCB 1 2 20 2 8 26 8 9 4 8 10 9 2 3 26 3 4 26 4 5 17 5 6 1 4 7 26 1 7 20 # 10 # bond angles # NBA 15 # IB JB KB MCB -1 1 2 30 1 2 8 12 2 8 10 18 2 8 9 29 9 8 10 32 1 2 3 12 3 2 8 12 2 3 4 12 3 4 5 12 3 4 7 12 # 10 4 5 6 11 5 4 7 12 1 7 4 12 2 1 7 20 -1 1 7 30 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 2 7 1 8 2 10 9 1 2 1 8 3 2 5 3 7 4 2 # dihedrals # NDA 8 # IB JB KB LB MCB -2 -1 1 2 4 -1 1 2 8 19 1 2 8 10 20 1 2 3 4 17 2 3 4 7 17 3 4 7 1 17 2 1 7 4 19 3 4 5 6 12 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE ILE # 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 5 14 -0.28000 0 4 2 3 4 8 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 1 6 4 5 6 8 9 10 4 CB 12 3 0.00000 0 4 5 6 7 8 5 CG1 13 4 0.00000 0 2 6 7 6 CG2 14 5 0.00000 0 0 7 CD 14 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 11 12 0.38000 0 9 O 1 16 -0.38000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 20 3 8 26 8 9 4 8 10 9 3 4 26 4 5 26 4 6 26 5 7 26 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 8 12 3 8 10 18 3 8 9 29 9 8 10 32 1 3 4 12 4 3 8 12 3 4 5 14 # 10 3 4 6 14 5 4 6 14 4 5 7 14 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 8 3 10 9 1 3 1 8 4 2 4 5 6 3 2 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 8 19 1 3 8 10 20 1 3 4 5 17 3 4 5 7 17 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE LEU # 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 5 14 -0.28000 0 4 2 3 4 8 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 8 9 10 4 CB 13 4 0.00000 1 4 5 6 7 8 5 CG 12 3 0.00000 0 2 6 7 6 CD1 14 5 0.00000 0 1 7 7 CD2 14 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 11 12 0.38000 0 9 O 1 16 -0.38000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 20 3 8 26 8 9 4 8 10 9 3 4 26 4 5 26 5 6 26 5 7 26 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 8 12 3 8 10 18 3 8 9 29 9 8 10 32 1 3 4 12 4 3 8 12 3 4 5 14 # 10 4 5 6 14 4 5 7 14 6 5 7 14 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 8 3 10 9 1 3 1 8 4 2 4 6 7 5 2 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 8 19 1 3 8 10 20 1 3 4 5 17 3 4 5 6 17 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE LYS # 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 5 14 -0.28000 0 4 2 3 4 11 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 11 12 13 4 CB 13 4 0.00000 1 3 5 6 11 5 CG 13 4 0.00000 0 2 6 7 6 CD 13 4 0.00000 1 2 7 8 7 CE 13 4 0.00000 0 3 8 9 10 8 NZ 6 14 -0.83000 0 2 9 10 9 HZ1 18 1 0.41500 0 1 10 10 HZ2 18 1 0.41500 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 11 C 11 12 0.38000 0 12 O 1 16 -0.38000 1 # bonds # NB 12 # IB JB MCB 1 2 2 1 3 20 3 11 26 11 12 4 11 13 9 3 4 26 4 5 26 5 6 26 6 7 26 7 8 20 # 10 8 9 2 8 10 2 # bond angles # NBA 16 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 11 12 3 11 13 18 3 11 12 29 12 11 13 32 1 3 4 12 4 3 11 12 3 4 5 14 # 10 4 5 6 14 5 6 7 14 6 7 8 14 7 8 9 10 7 8 10 10 9 8 10 9 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 11 3 13 12 1 3 1 11 4 2 # dihedrals # NDA 8 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 11 19 1 3 11 13 20 1 3 4 5 17 3 4 5 6 17 4 5 6 7 17 5 6 7 8 17 6 7 8 9 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE LYSH # 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 5 14 -0.28000 0 4 2 3 4 12 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 12 13 14 4 CB 13 4 0.00000 1 3 5 6 12 5 CG 13 4 0.00000 0 2 6 7 6 CD 13 4 0.00000 1 2 7 8 7 CE 13 4 0.00000 0 4 8 9 10 11 8 NZ 7 14 -0.74400 0 3 9 10 11 9 HZ1 18 1 0.24800 0 2 10 11 10 HZ2 18 1 0.24800 0 1 11 11 HZ3 18 1 0.24800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 12 C 11 12 0.38000 0 13 O 1 16 -0.38000 1 # bonds # NB 13 # IB JB MCB 1 2 2 1 3 20 3 12 26 12 13 4 12 14 9 3 4 26 4 5 26 5 6 26 6 7 26 7 8 20 # 10 8 9 2 8 10 2 8 11 2 # bond angles # NBA 19 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 12 12 3 12 14 18 3 12 13 29 13 12 14 32 1 3 4 12 4 3 12 12 3 4 5 14 # 10 4 5 6 14 5 6 7 14 6 7 8 14 7 8 9 10 7 8 10 10 7 8 11 10 9 8 10 9 9 8 11 9 10 8 11 9 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 12 3 14 13 1 3 1 12 4 2 # dihedrals # NDA 8 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 12 19 1 3 12 14 20 1 3 4 5 17 3 4 5 6 17 4 5 6 7 17 5 6 7 8 17 6 7 8 9 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE MET # 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 5 14 -0.28000 0 4 2 3 4 8 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 8 9 10 4 CB 13 4 0.00000 0 3 5 6 8 5 CG 13 4 0.00000 1 2 6 7 6 SD 20 32 0.00000 0 1 7 7 CE 14 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 11 12 0.38000 0 9 O 1 16 -0.38000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 20 3 8 26 8 9 4 8 10 9 3 4 26 4 5 26 5 6 30 6 7 29 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 8 12 3 8 10 18 3 8 9 29 9 8 10 32 1 3 4 12 4 3 8 12 3 4 5 14 # 10 4 5 6 15 5 6 7 3 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 8 3 10 9 1 3 1 8 4 2 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 8 19 1 3 8 10 20 1 3 4 5 17 3 4 5 6 17 4 5 6 7 13 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE PHE # 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 5 14 -0.28000 0 4 2 3 4 16 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 16 17 18 4 CB 13 4 0.00000 0 8 5 6 7 8 9 10 12 16 5 CG 11 12 0.00000 1 9 6 7 8 9 10 11 12 13 14 6 CD1 11 12 -0.10000 0 8 7 8 9 10 11 12 14 15 7 HD1 17 1 0.10000 1 4 8 10 11 14 8 CD2 11 12 -0.10000 0 6 9 10 12 13 14 15 9 HD2 17 1 0.10000 1 3 12 13 14 10 CE1 11 12 -0.10000 0 5 11 12 13 14 15 11 HE1 17 1 0.10000 1 3 12 14 15 12 CE2 11 12 -0.10000 0 3 13 14 15 13 HE2 17 1 0.10000 1 2 14 15 14 CZ 11 12 -0.10000 0 1 15 15 HZ 17 1 0.10000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 16 C 11 12 0.38000 0 17 O 1 16 -0.38000 1 # bonds # NB 18 # IB JB MCB 1 2 2 1 3 20 3 16 26 16 17 4 16 18 9 3 4 26 4 5 26 5 6 15 5 8 15 6 7 3 # 10 6 10 15 8 9 3 8 12 15 10 11 3 10 14 15 12 13 3 12 14 15 14 15 3 # bond angles # NBA 28 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 16 12 3 16 18 18 3 16 17 29 17 16 18 32 1 3 4 12 4 3 16 12 3 4 5 14 # 10 4 5 6 26 4 5 8 26 6 5 8 26 5 6 7 24 7 6 10 24 5 6 10 26 5 8 9 24 9 8 12 24 5 8 12 26 6 10 11 24 # 20 11 10 14 24 6 10 14 26 8 12 13 24 13 12 14 24 8 12 14 26 10 14 15 24 12 14 15 24 10 14 12 26 # improper dihedrals # NIDA 15 # IB JB KB LB MCB 1 -1 3 2 1 16 3 18 17 1 3 1 16 4 2 5 6 8 4 1 8 5 6 10 1 6 5 8 12 1 5 6 10 14 1 5 8 12 14 1 6 10 14 12 1 8 12 14 10 1 # 10 6 5 10 7 1 8 5 12 9 1 11 6 14 10 1 13 8 14 12 1 14 10 12 15 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 16 19 1 3 16 18 20 1 3 4 5 17 3 4 5 6 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE PRO # 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 5 14 0.00000 1 5 2 3 4 5 6 2 CA 12 3 0.00000 0 6 3 4 5 6 7 8 3 CB 13 4 0.00000 1 3 4 5 6 4 CG 13 4 0.00000 0 1 5 5 CD 13 4 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 11 12 0.38000 0 7 O 1 16 -0.38000 1 # bonds # NB 8 # IB JB MCB 1 2 20 2 6 26 6 7 4 6 8 9 2 3 26 3 4 26 4 5 26 1 5 20 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 30 1 2 6 12 2 6 8 18 2 6 7 29 7 6 8 32 1 2 3 12 3 2 6 12 2 3 4 12 3 4 5 12 1 5 4 12 # 10 2 1 5 20 -1 1 5 30 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 2 5 1 6 2 8 7 1 2 1 6 3 2 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 2 4 -1 1 2 6 19 1 2 6 8 20 1 2 3 4 17 2 3 4 5 17 3 4 5 1 17 2 1 5 4 19 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE SER # 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 5 14 -0.28000 0 4 2 3 4 7 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 1 5 4 5 7 8 9 4 CB 13 4 0.15000 0 3 5 6 7 5 OG 3 16 -0.54800 0 1 6 6 HG 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 7 C 11 12 0.38000 0 8 O 1 16 -0.38000 1 # bonds # NB 8 # IB JB MCB 1 2 2 1 3 20 3 7 26 7 8 4 7 9 9 3 4 26 4 5 17 5 6 1 # bond angles # NBA 11 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 7 12 3 7 9 18 3 7 8 29 8 7 9 32 1 3 4 12 4 3 7 12 3 4 5 12 # 10 4 5 6 11 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 7 3 9 8 1 3 1 7 4 2 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 7 19 1 3 7 9 20 1 3 4 5 17 3 4 5 6 12 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE THR # 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 5 14 -0.28000 0 4 2 3 4 8 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 1 6 4 5 7 8 9 10 4 CB 12 3 0.15000 0 4 5 6 7 8 5 OG1 3 16 -0.54800 0 2 6 7 6 HG1 18 1 0.39800 1 0 7 CG2 14 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 11 12 0.38000 0 9 O 1 16 -0.38000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 20 3 8 26 8 9 4 8 10 9 3 4 26 4 5 17 4 7 26 5 6 1 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 8 12 3 8 10 18 3 8 9 29 9 8 10 32 1 3 4 12 4 3 8 12 3 4 5 12 # 10 3 4 7 14 5 4 7 14 4 5 6 11 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 8 3 10 9 1 3 1 8 4 2 4 5 7 3 2 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 8 19 1 3 8 10 20 1 3 4 5 17 3 4 5 6 12 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE TRP # 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 5 14 -0.28000 0 4 2 3 4 20 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 20 21 22 4 CB 13 4 0.00000 1 8 5 6 7 8 9 11 12 20 5 CG 11 12 -0.14000 0 10 6 7 8 9 10 11 12 13 14 16 6 CD1 11 12 -0.10000 0 7 7 8 9 10 11 12 14 7 HD1 17 1 0.10000 0 4 8 9 10 11 8 CD2 11 12 0.00000 0 10 9 10 11 12 13 14 15 16 17 18 9 NE1 8 14 -0.05000 0 6 10 11 12 14 15 18 10 HE1 18 1 0.19000 0 2 11 14 11 CE2 11 12 0.00000 1 7 12 13 14 15 16 18 19 12 CE3 11 12 -0.10000 0 6 13 14 16 17 18 19 13 HE3 17 1 0.10000 1 3 16 17 18 14 CZ2 11 12 -0.10000 0 5 15 16 17 18 19 15 HZ2 17 1 0.10000 1 3 16 18 19 16 CZ3 11 12 -0.10000 0 3 17 18 19 17 HZ3 17 1 0.10000 1 2 18 19 18 CH2 11 12 -0.10000 0 1 19 19 HH2 17 1 0.10000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 20 C 11 12 0.38000 0 21 O 1 16 -0.38000 1 # bonds # NB 23 # IB JB MCB 1 2 2 1 3 20 3 20 26 20 21 4 20 22 9 3 4 26 4 5 26 5 6 9 5 8 15 6 7 3 # 10 6 9 9 8 11 15 8 12 15 9 10 2 9 11 9 11 14 15 12 13 3 12 16 15 14 15 3 14 18 15 # 20 16 17 3 16 18 15 18 19 3 # bond angles # NBA 37 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 20 12 3 20 22 18 3 20 21 29 21 20 22 32 1 3 4 12 4 3 20 12 3 4 5 14 # 10 4 5 6 36 4 5 8 36 6 5 8 6 5 6 7 35 7 6 9 35 5 6 9 6 5 8 11 6 6 9 11 6 6 9 10 35 10 9 11 35 # 20 8 11 9 6 5 8 12 38 9 11 14 38 8 11 14 26 11 8 12 26 8 12 13 24 13 12 16 24 8 12 16 26 11 14 15 24 15 14 18 24 # 30 11 14 18 26 12 16 17 24 17 16 18 24 12 16 18 26 14 18 19 24 16 18 19 24 14 18 16 26 # improper dihedrals # NIDA 23 # IB JB KB LB MCB 1 -1 3 2 1 20 3 22 21 1 3 1 20 4 2 5 6 8 4 1 8 5 6 9 1 6 5 8 11 1 5 6 9 11 1 5 8 11 9 1 6 9 11 8 1 6 5 9 7 1 # 10 9 6 11 10 1 8 11 12 5 1 11 8 14 9 1 12 8 11 14 1 8 11 14 18 1 11 8 12 16 1 11 14 18 16 1 8 12 16 18 1 12 16 18 14 1 12 8 16 13 1 # 20 14 11 18 15 1 16 12 18 17 1 18 14 16 19 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 20 19 1 3 20 22 20 1 3 4 5 17 3 4 5 8 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE TYR # 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 5 14 -0.28000 0 4 2 3 4 17 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 17 18 19 4 CB 13 4 0.00000 0 8 5 6 7 8 9 10 12 17 5 CG 11 12 0.00000 1 9 6 7 8 9 10 11 12 13 14 6 CD1 11 12 -0.10000 0 8 7 8 9 10 11 12 14 15 7 HD1 17 1 0.10000 1 4 8 10 11 14 8 CD2 11 12 -0.10000 0 6 9 10 12 13 14 15 9 HD2 17 1 0.10000 1 3 12 13 14 10 CE1 11 12 -0.10000 0 5 11 12 13 14 15 11 HE1 17 1 0.10000 1 3 12 14 15 12 CE2 11 12 -0.10000 0 3 13 14 15 13 HE2 17 1 0.10000 1 2 14 15 14 CZ 11 12 0.15000 0 2 15 16 15 OH 3 16 -0.54800 0 1 16 16 HH 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 17 C 11 12 0.38000 0 18 O 1 16 -0.38000 1 # bonds # NB 19 # IB JB MCB 1 2 2 1 3 20 3 17 26 17 18 4 17 19 9 3 4 26 4 5 26 5 6 15 5 8 15 6 7 3 # 10 6 10 15 8 9 3 8 12 15 10 11 3 10 14 15 12 13 3 12 14 15 14 15 12 15 16 1 # bond angles # NBA 29 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 17 12 3 17 19 18 3 17 18 29 18 17 19 32 1 3 4 12 4 3 17 12 3 4 5 14 # 10 4 5 6 26 4 5 8 26 6 5 8 26 5 6 7 24 7 6 10 24 5 6 10 26 5 8 9 24 9 8 12 24 5 8 12 26 6 10 11 24 # 20 11 10 14 24 6 10 14 26 8 12 13 24 13 12 14 24 8 12 14 26 10 14 12 26 10 14 15 26 12 14 15 26 14 15 16 11 # improper dihedrals # NIDA 15 # IB JB KB LB MCB 1 -1 3 2 1 17 3 19 18 1 3 1 17 4 2 5 6 8 4 1 8 5 6 10 1 6 5 8 12 1 5 6 10 14 1 5 8 12 14 1 6 10 14 12 1 8 12 14 10 1 # 10 6 5 10 7 1 8 5 12 9 1 11 6 14 10 1 13 8 14 12 1 14 10 12 15 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 17 19 1 3 17 19 20 1 3 4 5 17 3 4 5 6 20 10 14 15 16 2 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE VAL # 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 5 14 -0.28000 0 4 2 3 4 7 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 6 4 5 6 7 8 9 4 CB 12 3 0.00000 0 3 5 6 7 5 CG1 14 5 0.00000 0 1 6 6 CG2 14 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 7 C 11 12 0.38000 0 8 O 1 16 -0.38000 1 # bonds # NB 8 # IB JB MCB 1 2 2 1 3 20 3 7 26 7 8 4 7 9 9 3 4 26 4 5 26 4 6 26 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 7 12 3 7 9 18 3 7 8 29 8 7 9 32 1 3 4 12 4 3 7 12 3 4 5 14 # 10 3 4 6 14 5 4 6 14 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 7 3 9 8 1 3 1 7 4 2 3 5 6 4 2 # dihedrals # NDA 4 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 7 19 1 3 7 9 20 1 3 4 5 17 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE DALA # 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 5 14 -0.28000 0 4 2 3 4 5 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 4 4 5 6 7 4 CB 14 5 0.00000 1 1 5 # trailing atoms #ATOM ANM IACM MASS CGMICGM 5 C 11 12 0.38000 0 6 O 1 16 -0.38000 1 # bonds # NB 6 # IB JB MCB 1 2 2 1 3 20 3 5 26 5 6 4 5 7 9 3 4 26 # bond angles # NBA 9 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 5 12 3 5 7 18 3 5 6 29 6 5 7 32 1 3 4 12 4 3 5 12 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 5 3 7 6 1 4 1 5 3 2 # dihedrals # NDA 3 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 5 19 1 3 5 7 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE ABU # 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 5 14 -0.28000 0 4 2 3 4 6 2 H 18 1 0.28000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 6 7 8 4 CB 13 4 0.00000 0 2 5 6 5 CG 14 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 11 12 0.38000 0 7 O 1 16 -0.38000 1 # bonds # NB 7 # IB JB MCB 1 2 2 1 3 20 3 6 26 6 7 4 6 8 9 3 4 26 4 5 26 # bond angles # NBA 10 # IB JB KB MCB -1 1 2 31 2 1 3 17 -1 1 3 30 1 3 6 12 3 6 8 18 3 6 7 29 7 6 8 32 1 3 4 12 4 3 6 12 3 4 5 14 # 10 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 6 3 8 7 1 3 1 6 4 2 # dihedrals # NDA 4 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 6 19 1 3 6 8 20 1 3 4 5 17 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE MEBMT # 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 5 14 0.00000 0 4 2 3 4 13 2 CN 14 5 0.00000 1 1 3 3 CA 12 3 0.00000 1 6 4 5 7 13 14 15 4 CB 12 3 0.15000 0 6 5 6 7 8 9 13 5 OG1 3 16 -0.54800 0 2 6 7 6 HG1 18 1 0.39800 1 0 7 CG2 12 3 0.00000 0 3 8 9 10 8 CD1 14 5 0.00000 0 1 9 9 CD2 13 4 0.00000 1 2 10 11 10 CE 16 3 0.00000 0 2 11 12 11 CZ 16 3 0.00000 0 1 12 12 CH 14 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 13 C 11 12 0.38000 0 14 O 1 16 -0.38000 1 # bonds # NB 14 # IB JB MCB 1 2 20 1 3 20 3 13 26 13 14 4 13 15 9 3 4 26 4 5 17 5 6 1 4 7 26 7 8 26 # 10 7 9 26 9 10 26 10 11 9 11 12 26 # bond angles # NBA 19 # IB JB KB MCB -1 1 2 21 2 1 3 29 -1 1 3 30 1 3 13 12 3 13 15 18 3 13 14 29 14 13 15 32 1 3 4 12 4 3 13 12 3 4 5 12 # 10 3 4 7 14 5 4 7 14 4 5 6 11 4 7 8 14 4 7 9 14 8 7 9 14 7 9 10 14 9 10 11 26 10 11 12 26 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 1 -1 3 2 1 13 3 15 14 1 3 1 13 4 2 4 5 7 3 2 7 8 9 4 2 # dihedrals # NDA 9 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 13 19 1 3 13 15 20 1 3 4 7 17 3 4 5 6 12 3 4 7 9 17 4 7 9 10 17 7 9 10 11 20 9 10 11 12 4 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE MELEU # 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 5 14 0.00000 0 4 2 3 4 8 2 CN 14 5 0.00000 1 1 3 3 CA 12 3 0.00000 0 5 4 5 8 9 10 4 CB 13 4 0.00000 1 4 5 6 7 8 5 CG 12 3 0.00000 0 2 6 7 6 CD1 14 5 0.00000 0 1 7 7 CD2 14 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 11 12 0.38000 0 9 O 1 16 -0.38000 1 # bonds # NB 9 # IB JB MCB 1 2 20 1 3 20 3 8 26 8 9 4 8 10 9 3 4 26 4 5 26 5 6 26 5 7 26 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 21 2 1 3 29 -1 1 3 30 1 3 8 12 3 8 10 18 3 8 9 29 9 8 10 32 1 3 4 12 4 3 8 12 3 4 5 14 # 10 4 5 6 14 4 5 7 14 6 5 7 14 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 8 3 10 9 1 3 1 8 4 2 4 6 7 5 2 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 8 19 1 3 8 10 20 1 3 4 5 17 3 4 5 6 17 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE MEVAL # 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 5 14 0.00000 0 4 2 3 4 7 2 CN 14 5 0.00000 1 1 3 3 CA 12 3 0.00000 0 6 4 5 6 7 8 9 4 CB 12 3 0.00000 0 3 5 6 7 5 CG1 14 5 0.00000 0 1 6 6 CG2 14 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 7 C 11 12 0.38000 0 8 O 1 16 -0.38000 1 # bonds # NB 8 # IB JB MCB 1 2 20 1 3 20 3 7 26 7 8 4 7 9 9 3 4 26 4 5 26 4 6 26 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 21 2 1 3 29 -1 1 3 30 1 3 7 12 3 7 9 18 3 7 8 29 8 7 9 32 1 3 4 12 4 3 7 12 3 4 5 14 # 10 3 4 6 14 5 4 6 14 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 7 3 9 8 1 3 1 7 4 2 3 5 6 4 2 # dihedrals # NDA 4 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 7 19 1 3 7 9 20 1 3 4 5 17 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE SAR # 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 5 14 0.00000 0 3 2 3 4 2 CN 14 5 0.00000 1 1 3 3 CA 13 4 0.00000 1 3 4 5 6 # trailing atoms #ATOM ANM IACM MASS CGMICGM 4 C 11 12 0.38000 0 5 O 1 16 -0.38000 1 # bonds # NB 5 # IB JB MCB 1 2 20 1 3 20 3 4 26 4 5 4 4 6 9 # bond angles # NBA 7 # IB JB KB MCB -1 1 2 21 2 1 3 29 -1 1 3 30 1 3 4 12 3 4 6 18 3 4 5 29 5 4 6 32 # improper dihedrals # NIDA 2 # IB JB KB LB MCB 1 -1 3 2 1 4 3 6 5 1 # dihedrals # NDA 3 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 4 19 1 3 4 6 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE DADE # building block (residue, nucleotide, etc.) # RNME DADE # 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 27 31 1.44000 0 4 2 3 4 5 2 O1P 2 16 -0.36000 0 2 3 4 3 O2P 2 16 -0.36000 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 13 4 0.00000 1 3 6 7 22 6 C4* 12 3 0.16000 0 5 7 8 21 22 23 7 O4* 3 16 -0.36000 0 4 8 9 21 22 8 C1* 12 3 0.20000 1 8 9 10 11 18 19 20 21 22 9 N9 8 14 -0.20000 0 8 10 11 12 14 18 19 20 21 10 C4 11 12 0.20000 1 8 11 12 13 14 15 18 19 20 11 N3 8 14 -0.36000 0 6 12 13 14 18 19 20 12 C2 16 3 0.36000 1 4 13 14 15 18 13 N1 8 14 -0.36000 0 4 14 15 18 19 14 C6 11 12 0.36000 1 6 15 16 17 18 19 20 15 N6 6 14 -0.83000 0 4 16 17 18 19 16 H61 18 1 0.41500 0 1 17 17 H62 18 1 0.41500 1 0 18 C5 11 12 0.00000 0 2 19 20 19 N7 8 14 -0.36000 0 1 20 20 C8 16 3 0.36000 1 0 21 C2* 13 4 0.00000 0 2 22 23 # trailing atoms #ATOM ANM IACM MASS CGMICGM 22 C3* 12 3 0.00000 1 23 O3* 3 16 -0.36000 0 # bonds # NB 26 # IB JB MCB 1 2 23 1 3 23 1 4 27 4 5 19 5 6 25 6 7 19 6 22 25 7 8 19 8 9 21 8 21 25 # 10 9 10 9 9 20 9 10 11 11 10 18 15 11 12 6 12 13 6 13 14 11 14 15 8 14 18 15 15 16 2 # 20 15 17 2 18 19 9 19 20 9 21 22 25 22 23 19 23 24 27 # bond angles # NBA 40 # IB JB KB MCB 0 1 2 13 0 1 3 13 0 1 4 4 2 1 3 28 2 1 4 13 3 1 4 13 1 4 5 25 4 5 6 8 5 6 7 8 5 6 22 7 # 10 7 6 22 8 6 7 8 9 7 8 9 8 7 8 21 8 9 8 21 8 8 9 10 36 8 9 20 36 10 9 20 6 9 10 11 38 9 10 18 6 # 20 11 10 18 26 10 11 12 26 11 12 13 26 12 13 14 26 13 14 15 26 13 14 18 26 15 14 18 26 14 15 16 22 14 15 17 22 16 15 17 23 # 30 10 18 14 26 10 18 19 6 14 18 19 38 18 19 20 6 9 20 19 6 8 21 22 7 6 22 21 7 6 22 23 8 21 22 23 8 22 23 24 25 # 40 # improper dihedrals # NIDA 19 # IB JB KB LB MCB 22 5 7 6 2 22 21 23 6 2 21 7 9 8 2 8 10 20 9 1 10 9 20 19 1 20 9 10 18 1 18 19 20 9 1 9 10 18 19 1 10 18 19 20 1 10 9 11 18 1 # 10 18 14 19 10 1 11 10 18 14 1 13 14 18 10 1 18 10 11 12 1 12 13 14 18 1 10 11 12 13 1 11 12 13 14 1 15 13 18 14 1 15 16 17 14 1 # dihedrals # NDA 21 # IB JB KB LB MCB -1 0 1 4 11 -1 0 1 4 9 0 1 4 5 11 0 1 4 5 9 1 4 5 6 14 4 5 6 22 17 4 5 6 22 7 4 5 6 7 8 5 6 22 21 17 5 6 22 23 7 # 10 7 6 22 21 7 7 6 22 23 8 8 21 22 6 17 8 21 22 23 7 7 8 21 22 17 7 8 21 22 7 22 6 7 8 14 6 7 8 21 14 7 8 9 10 6 18 14 15 16 4 # 20 6 22 23 24 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE DGUA # building block (residue, nucleotide, etc.) # RNME DGUA # 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 27 31 1.44000 0 4 2 3 4 5 2 O1P 2 16 -0.36000 0 2 3 4 3 O2P 2 16 -0.36000 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 13 4 0.00000 1 3 6 7 24 6 C4* 12 3 0.16000 0 5 7 8 23 24 25 7 O4* 3 16 -0.36000 0 4 8 9 23 24 8 C1* 12 3 0.20000 1 8 9 10 11 20 21 22 23 24 9 N9 8 14 -0.20000 0 8 10 11 12 18 20 21 22 23 10 C4 11 12 0.20000 1 9 11 12 13 16 18 19 20 21 22 11 N3 8 14 -0.36000 0 8 12 13 16 17 18 20 21 22 12 C2 11 12 0.36000 1 8 13 14 15 16 17 18 19 20 13 N2 6 14 -0.83000 0 5 14 15 16 17 18 14 H21 18 1 0.41500 0 1 15 15 H22 18 1 0.41500 1 0 16 N1 8 14 -0.28000 0 5 17 18 19 20 21 17 H1 18 1 0.28000 1 3 18 19 20 18 C6 11 12 0.38000 0 4 19 20 21 22 19 O6 1 16 -0.38000 1 2 20 21 20 C5 11 12 0.00000 0 2 21 22 21 N7 8 14 -0.36000 0 1 22 22 C8 16 3 0.36000 1 0 23 C2* 13 4 0.00000 0 2 24 25 # trailing atoms #ATOM ANM IACM MASS CGMICGM 24 C3* 12 3 0.00000 1 25 O3* 3 16 -0.36000 0 # bonds # NB 28 # IB JB MCB 1 2 23 1 3 23 1 4 27 4 5 19 5 6 25 6 7 19 6 24 25 7 8 19 8 9 21 8 23 25 # 10 9 10 9 9 22 9 10 11 11 10 20 15 11 12 11 12 13 8 12 16 16 13 14 2 13 15 2 16 17 2 # 20 16 18 16 18 19 4 18 20 15 20 21 9 21 22 9 23 24 25 24 25 19 25 26 27 # bond angles # NBA 44 # IB JB KB MCB 0 1 2 13 0 1 3 13 0 1 4 4 2 1 3 28 2 1 4 13 3 1 4 13 1 4 5 25 4 5 6 8 5 6 7 8 5 6 24 7 # 10 7 6 24 8 6 7 8 9 7 8 9 8 7 8 23 8 9 8 23 8 8 9 10 36 8 9 22 36 10 9 22 6 9 10 11 38 9 10 20 6 # 20 11 10 20 26 10 11 12 26 11 12 13 26 11 12 16 26 13 12 16 26 12 13 14 22 12 13 15 22 14 13 15 23 12 16 17 24 12 16 18 26 # 30 17 16 18 24 16 18 19 26 16 18 20 26 19 18 20 26 10 20 18 26 10 20 21 6 18 20 21 38 20 21 22 6 9 22 21 6 8 23 24 7 # 40 6 24 23 7 6 24 25 8 23 24 25 8 24 25 26 25 # improper dihedrals # NIDA 21 # IB JB KB LB MCB 24 5 7 6 2 24 23 25 6 2 23 7 9 8 2 8 10 22 9 1 10 9 22 21 1 22 9 10 20 1 20 21 22 9 1 9 10 20 21 1 10 20 21 22 1 10 9 11 20 1 # 10 20 18 21 10 1 11 10 20 18 1 16 18 20 10 1 20 10 11 12 1 12 16 18 20 1 10 11 12 16 1 11 12 16 18 1 13 11 16 12 1 13 14 15 12 1 17 12 18 16 1 # 20 19 16 20 18 1 # dihedrals # NDA 21 # IB JB KB LB MCB -1 0 1 4 11 -1 0 1 4 9 0 1 4 5 11 0 1 4 5 9 1 4 5 6 14 4 5 6 24 17 4 5 6 24 7 4 5 6 7 8 5 6 24 23 17 5 6 24 25 7 # 10 7 6 24 23 7 7 6 24 25 8 8 23 24 6 17 8 23 24 25 7 7 8 23 24 17 7 8 23 24 7 24 6 7 8 14 6 7 8 23 14 7 8 9 10 6 11 12 13 14 4 # 20 6 24 25 26 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE DCYT # building block (residue, nucleotide, etc.) # RNME DCYT # number of atoms, number of preceding exclusions # NMAT NLIN 21 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 27 31 1.44000 0 4 2 3 4 5 2 O1P 2 16 -0.36000 0 2 3 4 3 O2P 2 16 -0.36000 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 13 4 0.00000 1 3 6 7 20 6 C4* 12 3 0.16000 0 5 7 8 19 20 21 7 O4* 3 16 -0.36000 0 4 8 9 19 20 8 C1* 12 3 0.20000 1 8 9 10 11 12 13 18 19 20 9 N1 8 14 -0.20000 0 7 10 11 12 13 14 18 19 10 C6 16 3 0.20000 1 6 11 12 13 14 15 18 11 C2 11 12 0.38000 0 5 12 13 14 15 18 12 O2 1 16 -0.38000 1 2 13 14 13 N3 8 14 -0.36000 0 3 14 15 18 14 C4 11 12 0.36000 1 4 15 16 17 18 15 N4 6 14 -0.83000 0 3 16 17 18 16 H41 18 1 0.41500 0 1 17 17 H42 18 1 0.41500 1 0 18 C5 16 3 0.00000 1 0 19 C2* 13 4 0.00000 0 2 20 21 # trailing atoms #ATOM ANM IACM MASS CGMICGM 20 C3* 12 3 0.00000 1 21 O3* 3 16 -0.36000 0 # bonds # NB 23 # IB JB MCB 1 2 23 1 3 23 1 4 27 4 5 19 5 6 25 6 7 19 6 20 25 7 8 19 8 9 22 8 19 25 # 10 9 10 16 9 11 16 10 18 15 11 12 4 11 13 11 13 14 11 14 15 8 14 18 15 15 16 2 15 17 2 # 20 19 20 25 20 21 19 21 22 27 # bond angles # NBA 35 # IB JB KB MCB 0 1 2 13 0 1 3 13 0 1 4 4 2 1 3 28 2 1 4 13 3 1 4 13 1 4 5 25 4 5 6 8 5 6 7 8 5 6 20 7 # 10 7 6 20 8 6 7 8 9 7 8 9 8 7 8 19 8 9 8 19 7 8 9 10 26 8 9 11 26 10 9 11 26 9 10 18 26 9 11 12 26 # 20 9 11 13 26 12 11 13 26 11 13 14 26 13 14 15 26 13 14 18 26 15 14 18 26 14 15 16 22 14 15 17 22 16 15 17 23 10 18 14 26 # 30 8 19 20 7 6 20 19 7 6 20 21 8 19 20 21 8 20 21 22 25 # improper dihedrals # NIDA 13 # IB JB KB LB MCB 20 5 7 6 2 20 19 21 6 2 19 7 9 8 2 9 10 11 8 1 11 9 10 18 1 10 9 11 13 1 9 10 18 14 1 9 11 13 14 1 13 14 18 10 1 11 13 14 18 1 # 10 12 9 13 11 1 15 13 18 14 1 15 16 17 14 1 # dihedrals # NDA 21 # IB JB KB LB MCB -1 0 1 4 11 -1 0 1 4 9 0 1 4 5 11 0 1 4 5 9 1 4 5 6 14 4 5 6 20 17 4 5 6 20 7 4 5 6 7 8 5 6 20 19 17 5 6 20 21 7 # 10 7 6 20 19 7 7 6 20 21 8 8 19 20 6 17 8 19 20 21 7 7 8 19 20 17 7 8 19 20 7 20 6 7 8 14 6 7 8 19 14 7 8 9 11 6 13 14 15 16 4 # 20 6 20 21 22 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE DTHY # building block (residue, nucleotide, etc.) # RNME DTHY # number of atoms, number of preceding exclusions # NMAT NLIN 21 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 27 31 1.44000 0 4 2 3 4 5 2 O1P 2 16 -0.36000 0 2 3 4 3 O2P 2 16 -0.36000 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 13 4 0.00000 1 3 6 7 20 6 C4* 12 3 0.16000 0 5 7 8 19 20 21 7 O4* 3 16 -0.36000 0 4 8 9 19 20 8 C1* 12 3 0.20000 1 8 9 10 11 12 13 17 19 20 9 N1 8 14 -0.20000 0 9 10 11 12 13 14 15 17 18 19 10 C6 16 3 0.20000 1 7 11 12 13 15 16 17 18 11 C2 11 12 0.38000 0 6 12 13 14 15 16 17 12 O2 1 16 -0.38000 1 3 13 14 15 13 N3 8 14 -0.28000 0 5 14 15 16 17 18 14 H3 18 1 0.28000 1 3 15 16 17 15 C4 11 12 0.38000 0 3 16 17 18 16 O4 1 16 -0.38000 1 2 17 18 17 C5 11 12 0.00000 0 1 18 18 C5M 14 5 0.00000 1 0 19 C2* 13 4 0.00000 0 2 20 21 # trailing atoms #ATOM ANM IACM MASS CGMICGM 20 C3* 12 3 0.00000 1 21 O3* 3 16 -0.36000 0 # bonds # NB 23 # IB JB MCB 1 2 23 1 3 23 1 4 27 4 5 19 5 6 25 6 7 19 6 20 25 7 8 19 8 9 22 8 19 25 # 10 9 10 16 9 11 16 10 17 15 11 12 4 11 13 16 13 14 2 13 15 16 15 16 4 15 17 15 17 18 26 # 20 19 20 25 20 21 19 21 22 27 # bond angles # NBA 36 # IB JB KB MCB 0 1 2 13 0 1 3 13 0 1 4 4 2 1 3 28 2 1 4 13 3 1 4 13 1 4 5 25 4 5 6 8 5 6 7 8 5 6 20 7 # 10 7 6 20 8 6 7 8 9 7 8 9 8 7 8 19 8 9 8 19 7 8 9 10 26 8 9 11 26 10 9 11 26 9 10 17 26 9 11 12 26 # 20 9 11 13 26 12 11 13 26 11 13 14 24 11 13 15 26 14 13 15 24 13 15 16 26 13 15 17 26 16 15 17 26 10 17 15 26 10 17 18 26 # 30 15 17 18 26 8 19 20 7 6 20 19 7 6 20 21 8 19 20 21 8 20 21 22 25 # improper dihedrals # NIDA 14 # IB JB KB LB MCB 20 5 7 6 2 20 19 21 6 2 19 7 9 8 2 9 10 11 8 1 11 9 10 17 1 10 9 11 13 1 9 10 17 15 1 9 11 13 15 1 13 15 17 10 1 11 13 15 17 1 # 10 12 9 13 11 1 14 11 15 13 1 16 13 17 15 1 17 10 15 18 1 # dihedrals # NDA 20 # IB JB KB LB MCB -1 0 1 4 11 -1 0 1 4 9 0 1 4 5 11 0 1 4 5 9 1 4 5 6 14 4 5 6 20 17 4 5 6 20 7 4 5 6 7 8 5 6 20 19 17 5 6 20 21 7 # 10 7 6 20 19 7 7 6 20 21 8 8 19 20 6 17 8 19 20 21 7 7 8 19 20 17 7 8 19 20 7 20 6 7 8 14 6 7 8 19 14 7 8 9 11 6 6 20 21 22 14 # 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE ADE # building block (residue, nucleotide, etc.) # RNME ADE # 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 27 31 1.44000 0 4 2 3 4 5 2 O1P 2 16 -0.36000 0 2 3 4 3 O2P 2 16 -0.36000 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 13 4 0.00000 1 3 6 7 24 6 C4* 12 3 0.16000 0 5 7 8 21 24 25 7 O4* 3 16 -0.36000 0 4 8 9 21 24 8 C1* 12 3 0.20000 1 9 9 10 11 18 19 20 21 22 24 9 N9 8 14 -0.20000 0 8 10 11 12 14 18 19 20 21 10 C4 11 12 0.20000 1 8 11 12 13 14 15 18 19 20 11 N3 8 14 -0.36000 0 6 12 13 14 18 19 20 12 C2 16 3 0.36000 1 4 13 14 15 18 13 N1 8 14 -0.36000 0 4 14 15 18 19 14 C6 11 12 0.36000 1 6 15 16 17 18 19 20 15 N6 6 14 -0.83000 0 4 16 17 18 19 16 H61 18 1 0.41500 0 1 17 17 H62 18 1 0.41500 1 0 18 C5 11 12 0.00000 0 2 19 20 19 N7 8 14 -0.36000 0 1 20 20 C8 16 3 0.36000 1 0 21 C2* 12 3 0.15000 0 4 22 23 24 25 22 O2* 3 16 -0.54800 0 2 23 24 23 H2* 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 24 C3* 12 3 0.00000 1 25 O3* 3 16 -0.36000 0 # bonds # NB 28 # IB JB MCB 1 2 23 1 3 23 1 4 27 4 5 19 5 6 25 6 7 19 6 24 25 7 8 19 8 9 21 8 21 25 # 10 9 10 9 9 20 9 10 11 11 10 18 15 11 12 6 12 13 6 13 14 11 14 15 8 14 18 15 15 16 2 # 20 15 17 2 18 19 9 19 20 9 21 22 19 22 23 1 21 24 25 24 25 19 25 26 27 # bond angles # NBA 43 # IB JB KB MCB 0 1 2 13 0 1 3 13 0 1 4 4 2 1 3 28 2 1 4 13 3 1 4 13 1 4 5 25 4 5 6 8 5 6 7 8 5 6 24 7 # 10 7 6 24 8 6 7 8 9 7 8 9 8 7 8 21 8 9 8 21 8 8 9 10 36 8 9 20 36 10 9 20 6 9 10 11 38 9 10 18 6 # 20 11 10 18 26 10 11 12 26 11 12 13 26 12 13 14 26 13 14 15 26 13 14 18 26 15 14 18 26 14 15 16 22 14 15 17 22 16 15 17 23 # 30 10 18 14 26 10 18 19 6 14 18 19 38 18 19 20 6 9 20 19 6 8 21 24 7 8 21 22 8 22 21 24 8 21 22 23 11 6 24 21 7 # 40 6 24 25 8 21 24 25 8 24 25 26 25 # improper dihedrals # NIDA 20 # IB JB KB LB MCB 24 5 7 6 2 24 21 25 6 2 21 7 9 8 2 8 10 20 9 1 10 9 20 19 1 20 9 10 18 1 18 19 20 9 1 9 10 18 19 1 10 18 19 20 1 10 9 11 18 1 # 10 18 14 19 10 1 11 10 18 14 1 13 14 18 10 1 18 10 11 12 1 12 13 14 18 1 10 11 12 13 1 11 12 13 14 1 15 13 18 14 1 15 16 17 14 1 21 22 24 8 2 # dihedrals # NDA 26 # IB JB KB LB MCB -1 0 1 4 11 -1 0 1 4 9 0 1 4 5 11 0 1 4 5 9 1 4 5 6 14 4 5 6 24 17 4 5 6 24 7 4 5 6 7 8 5 6 24 21 17 5 6 24 25 7 # 10 7 6 24 21 7 7 6 24 25 8 8 21 24 6 17 8 21 24 25 7 22 21 24 6 7 22 21 24 25 8 7 8 21 24 17 7 8 21 24 7 9 8 21 22 7 7 8 21 22 8 # 20 8 21 22 23 12 24 6 7 8 14 6 7 8 21 14 7 8 9 10 6 18 14 15 16 4 6 24 25 26 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE GUA # building block (residue, nucleotide, etc.) # RNME GUA # 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 27 31 1.44000 0 4 2 3 4 5 2 O1P 2 16 -0.36000 0 2 3 4 3 O2P 2 16 -0.36000 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 13 4 0.00000 1 3 6 7 26 6 C4* 12 3 0.16000 0 5 7 8 23 26 27 7 O4* 3 16 -0.36000 0 4 8 9 23 26 8 C1* 12 3 0.20000 1 9 9 10 11 20 21 22 23 24 26 9 N9 8 14 -0.20000 0 8 10 11 12 18 20 21 22 23 10 C4 11 12 0.20000 1 9 11 12 13 16 18 19 20 21 22 11 N3 8 14 -0.36000 0 8 12 13 16 17 18 20 21 22 12 C2 11 12 0.36000 1 8 13 14 15 16 17 18 19 20 13 N2 6 14 -0.83000 0 5 14 15 16 17 18 14 H21 18 1 0.41500 0 1 15 15 H22 18 1 0.41500 1 0 16 N1 8 14 -0.28000 0 5 17 18 19 20 21 17 H1 18 1 0.28000 1 3 18 19 20 18 C6 11 12 0.38000 0 4 19 20 21 22 19 O6 1 16 -0.38000 1 2 20 21 20 C5 11 12 0.00000 0 2 21 22 21 N7 8 14 -0.36000 0 1 22 22 C8 16 3 0.36000 1 0 23 C2* 12 3 0.15000 0 4 24 25 26 27 24 O2* 3 16 -0.54800 0 2 25 26 25 H2* 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 26 C3* 12 3 0.00000 1 27 O3* 3 16 -0.36000 0 # bonds # NB 30 # IB JB MCB 1 2 23 1 3 23 1 4 27 4 5 19 5 6 25 6 7 19 6 26 25 7 8 19 8 9 21 8 23 25 # 10 9 10 9 9 22 9 10 11 11 10 20 15 11 12 11 12 13 8 12 16 16 13 14 2 13 15 2 16 17 2 # 20 16 18 16 18 19 4 18 20 15 20 21 9 21 22 9 23 24 19 24 25 1 23 26 25 26 27 19 27 28 27 # bond angles # NBA 47 # IB JB KB MCB 0 1 2 13 0 1 3 13 0 1 4 4 2 1 3 28 2 1 4 13 3 1 4 13 1 4 5 25 4 5 6 8 5 6 7 8 5 6 26 7 # 10 7 6 26 8 6 7 8 9 7 8 9 8 7 8 23 8 9 8 23 8 8 9 10 36 8 9 22 36 10 9 22 6 9 10 11 38 9 10 20 6 # 20 11 10 20 26 10 11 12 26 11 12 13 26 11 12 16 26 13 12 16 26 12 13 14 22 12 13 15 22 14 13 15 23 12 16 17 24 12 16 18 26 # 30 17 16 18 24 16 18 19 26 16 18 20 26 19 18 20 26 10 20 18 26 10 20 21 6 18 20 21 38 20 21 22 6 9 22 21 6 8 23 26 7 # 40 8 23 24 8 24 23 26 8 23 24 25 11 6 26 23 7 6 26 27 8 23 26 27 8 26 27 28 25 # improper dihedrals # NIDA 22 # IB JB KB LB MCB 26 5 7 6 2 26 23 27 6 2 23 7 9 8 2 8 10 22 9 1 10 9 22 21 1 22 9 10 20 1 20 21 22 9 1 9 10 20 21 1 10 20 21 22 1 10 9 11 20 1 # 10 20 18 21 10 1 11 10 20 18 1 16 18 20 10 1 20 10 11 12 1 12 16 18 20 1 10 11 12 16 1 11 12 16 18 1 13 11 16 12 1 13 14 15 12 1 17 12 18 16 1 # 20 19 16 20 18 1 23 24 26 8 2 # dihedrals # NDA 26 # IB JB KB LB MCB -1 0 1 4 11 -1 0 1 4 9 0 1 4 5 11 0 1 4 5 9 1 4 5 6 14 4 5 6 26 17 4 5 6 26 7 4 5 6 7 8 5 6 26 23 17 5 6 26 27 7 # 10 7 6 26 23 7 7 6 26 27 8 8 23 26 6 17 8 23 26 27 7 24 23 26 6 7 24 23 26 27 8 7 8 23 26 17 7 8 23 26 7 9 8 23 24 7 7 8 23 24 8 # 20 8 23 24 25 12 26 6 7 8 14 6 7 8 23 14 7 8 9 10 6 11 12 13 14 4 6 26 27 28 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE CYT # building block (residue, nucleotide, etc.) # RNME CYT # 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 27 31 1.44000 0 4 2 3 4 5 2 O1P 2 16 -0.36000 0 2 3 4 3 O2P 2 16 -0.36000 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 13 4 0.00000 1 3 6 7 22 6 C4* 12 3 0.16000 0 5 7 8 19 22 23 7 O4* 3 16 -0.36000 0 4 8 9 19 22 8 C1* 12 3 0.20000 1 9 9 10 11 12 13 18 19 20 22 9 N1 8 14 -0.20000 0 7 10 11 12 13 14 18 19 10 C6 16 3 0.20000 1 6 11 12 13 14 15 18 11 C2 11 12 0.38000 0 5 12 13 14 15 18 12 O2 1 16 -0.38000 1 2 13 14 13 N3 8 14 -0.36000 0 3 14 15 18 14 C4 11 12 0.36000 1 4 15 16 17 18 15 N4 6 14 -0.83000 0 3 16 17 18 16 H41 18 1 0.41500 0 1 17 17 H42 18 1 0.41500 1 0 18 C5 16 3 0.00000 1 0 19 C2* 12 3 0.15000 0 4 20 21 22 23 20 O2* 3 16 -0.54800 0 2 21 22 21 H2* 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 22 C3* 12 3 0.00000 1 23 O3* 3 16 -0.36000 0 # bonds # NB 25 # IB JB MCB 1 2 23 1 3 23 1 4 27 4 5 19 5 6 25 6 7 19 6 22 25 7 8 19 8 9 22 8 19 25 # 10 9 10 16 9 11 16 10 18 15 11 12 4 11 13 11 13 14 11 14 15 8 14 18 15 15 16 2 15 17 2 # 20 19 20 19 20 21 1 19 22 25 22 23 19 23 24 27 # bond angles # NBA 38 # IB JB KB MCB 0 1 2 13 0 1 3 13 0 1 4 4 2 1 3 28 2 1 4 13 3 1 4 13 1 4 5 25 4 5 6 8 5 6 7 8 5 6 22 7 # 10 7 6 22 8 6 7 8 9 7 8 9 8 7 8 19 8 9 8 19 7 8 9 10 26 8 9 11 26 10 9 11 26 9 10 18 26 9 11 12 26 # 20 9 11 13 26 12 11 13 26 11 13 14 26 13 14 15 26 13 14 18 26 15 14 18 26 14 15 16 22 14 15 17 22 16 15 17 23 10 18 14 26 # 30 8 19 22 7 8 19 20 8 20 19 22 8 19 20 21 11 6 22 19 7 6 22 23 8 19 22 23 8 22 23 24 25 # improper dihedrals # NIDA 14 # IB JB KB LB MCB 22 5 7 6 2 22 19 23 6 2 19 7 9 8 2 9 10 11 8 1 11 9 10 18 1 10 9 11 13 1 9 10 18 14 1 9 11 13 14 1 13 14 18 10 1 11 13 14 18 1 # 10 12 9 13 11 1 15 13 18 14 1 15 16 17 14 1 19 20 22 8 2 # dihedrals # NDA 26 # IB JB KB LB MCB -1 0 1 4 11 -1 0 1 4 9 0 1 4 5 11 0 1 4 5 9 1 4 5 6 14 4 5 6 22 17 4 5 6 22 7 4 5 6 7 8 5 6 22 19 17 5 6 22 23 7 # 10 7 6 22 19 7 7 6 22 23 8 8 19 22 6 17 8 19 22 23 7 20 19 22 6 7 20 19 22 23 8 7 8 19 22 17 7 8 19 22 7 9 8 19 20 7 7 8 19 20 8 # 20 8 19 20 21 12 22 6 7 8 14 6 7 8 19 14 7 8 9 11 6 13 14 15 16 4 6 22 23 24 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE URA # building block (residue, nucleotide, etc.) # RNME URA # 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 27 31 1.44000 0 4 2 3 4 5 2 O1P 2 16 -0.36000 0 2 3 4 3 O2P 2 16 -0.36000 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 13 4 0.00000 1 3 6 7 21 6 C4* 12 3 0.16000 0 5 7 8 18 21 22 7 O4* 3 16 -0.36000 0 4 8 9 18 21 8 C1* 12 3 0.20000 1 9 9 10 11 12 13 17 18 19 21 9 N1 8 14 -0.20000 0 8 10 11 12 13 14 15 17 18 10 C6 16 3 0.20000 1 6 11 12 13 15 16 17 11 C2 11 12 0.38000 0 6 12 13 14 15 16 17 12 O2 1 16 -0.38000 1 3 13 14 15 13 N3 8 14 -0.28000 0 4 14 15 16 17 14 H3 18 1 0.28000 1 3 15 16 17 15 C4 11 12 0.38000 0 2 16 17 16 O4 1 16 -0.38000 1 1 17 17 C5 16 3 0.00000 1 0 18 C2* 12 3 0.15000 0 4 19 20 21 22 19 O2* 3 16 -0.54800 0 2 20 21 20 H2* 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 21 C3* 12 3 0.00000 1 22 O3* 3 16 -0.36000 0 # bonds # NB 24 # IB JB MCB 1 2 23 1 3 23 1 4 27 4 5 19 5 6 25 6 7 19 6 21 25 7 8 19 8 9 22 8 18 25 # 10 9 10 16 9 11 16 10 17 15 11 12 4 11 13 16 13 14 2 13 15 16 15 16 4 15 17 15 18 19 19 # 20 19 20 1 18 21 25 21 22 19 22 23 27 # bond angles # NBA 37 # IB JB KB MCB 0 1 2 13 0 1 3 13 0 1 4 4 2 1 3 28 2 1 4 13 3 1 4 13 1 4 5 25 4 5 6 8 5 6 7 8 5 6 21 7 # 10 7 6 21 8 6 7 8 9 7 8 9 8 7 8 18 8 9 8 18 7 8 9 10 26 8 9 11 26 10 9 11 26 9 10 17 26 9 11 12 26 # 20 9 11 13 26 12 11 13 26 11 13 14 24 11 13 15 26 14 13 15 24 13 15 16 26 13 15 17 26 16 15 17 26 10 17 15 26 8 18 21 7 # 30 8 18 19 8 19 18 21 8 18 19 20 11 6 21 18 7 6 21 22 8 18 21 22 8 21 22 23 25 # improper dihedrals # NIDA 14 # IB JB KB LB MCB 21 5 7 6 2 21 18 22 6 2 18 7 9 8 2 9 10 11 8 1 11 9 10 17 1 10 9 11 13 1 9 10 17 15 1 9 11 13 15 1 13 15 17 10 1 11 13 15 17 1 # 10 12 9 13 11 1 14 11 15 13 1 16 13 17 15 1 18 19 21 8 2 # dihedrals # NDA 25 # IB JB KB LB MCB -1 0 1 4 11 -1 0 1 4 9 0 1 4 5 11 0 1 4 5 9 1 4 5 6 14 4 5 6 21 17 4 5 6 21 7 4 5 6 7 8 5 6 21 18 17 5 6 21 22 7 # 10 7 6 21 18 7 7 6 21 22 8 8 18 21 6 17 8 18 21 22 7 19 18 21 6 7 19 18 21 22 8 7 8 18 21 17 7 8 18 21 7 9 8 18 19 7 7 8 18 19 8 # 20 8 18 19 20 12 21 6 7 8 14 6 7 8 18 14 7 8 9 11 6 6 21 22 23 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE FMNO # building block (residue, nucleotide, etc.) # RNME FMNO # number of atoms, number of preceding exclusions # NMAT NLIN 36 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 FC9A 11 12 0.20000 0 12 2 3 4 11 12 13 14 15 17 18 19 20 2 FN10 8 14 -0.20000 1 12 3 4 5 9 11 12 13 14 17 19 20 21 3 FC10A 11 12 0.36000 0 11 4 5 6 7 9 10 11 12 13 19 20 4 FN1 8 14 -0.36000 1 8 5 6 7 8 9 11 12 20 5 FC2 11 12 0.38000 0 6 6 7 8 9 10 11 6 FO2 1 16 -0.38000 1 3 7 8 9 7 FN3 8 14 -0.28000 0 5 8 9 10 11 12 8 FH3 18 1 0.28000 1 3 9 10 11 9 FC4 11 12 0.38000 0 4 10 11 12 13 10 FO4 1 16 -0.38000 1 2 11 12 11 FC4A 11 12 0.18000 0 4 12 13 14 20 12 FN5 8 14 -0.28000 0 4 13 14 15 19 13 FC5A 11 12 0.10000 1 6 14 15 16 17 19 20 14 FC6 16 3 0.00000 1 5 15 16 17 18 19 15 FC7 11 12 0.00000 0 4 16 17 18 19 16 FCM7 14 5 0.00000 1 3 17 18 19 17 FC8 11 12 0.00000 0 2 18 19 18 FCM8 14 5 0.00000 1 1 19 19 FC9 16 3 0.00000 1 1 20 20 FCA 13 4 0.00000 1 3 21 22 24 21 FCB 12 3 0.15000 0 5 22 23 24 25 27 22 FOB 3 16 -0.54800 0 2 23 24 23 FHB 18 1 0.39800 1 0 24 FCG 12 3 0.15000 0 5 25 26 27 28 30 25 FOG 3 16 -0.54800 0 2 26 27 26 FHG 18 1 0.39800 1 0 27 FCD 12 3 0.15000 0 4 28 29 30 31 28 FOD 3 16 -0.54800 0 2 29 30 29 FHD 18 1 0.39800 1 0 30 FCE 13 4 0.15000 0 2 31 32 31 FOZ 3 16 -0.36000 0 5 32 33 34 35 36 32 FPH 27 31 1.08000 0 4 33 34 35 36 33 FOH 3 16 -0.54800 0 3 34 35 36 34 FHH 18 1 0.39800 0 2 35 36 35 FOT1 2 16 -0.36000 0 1 36 36 FOT2 2 16 -0.36000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 38 # IB JB MCB 1 2 16 1 13 15 1 19 15 2 3 16 2 20 22 3 4 11 3 11 15 4 5 11 5 6 4 5 7 16 # 10 7 8 2 7 9 16 9 10 4 9 11 15 11 12 11 12 13 11 13 14 15 14 15 15 15 16 26 15 17 15 # 20 17 18 26 17 19 15 20 21 26 21 22 17 21 24 26 22 23 1 24 25 17 24 27 26 25 26 1 27 28 17 # 30 27 30 26 28 29 1 30 31 17 31 32 27 32 33 27 32 35 23 32 36 23 33 34 1 # bond angles # NBA 56 # IB JB KB MCB 2 1 13 26 2 1 19 26 13 1 19 26 1 2 3 26 1 2 20 26 3 2 20 26 2 3 4 26 2 3 11 26 4 3 11 26 3 4 5 26 # 10 4 5 6 26 4 5 7 26 6 5 7 26 5 7 8 24 5 7 9 26 8 7 9 24 7 9 10 26 7 9 11 26 10 9 11 26 3 11 9 26 # 20 3 11 12 26 9 11 12 26 11 12 13 26 1 13 12 26 1 13 14 26 12 13 14 26 13 14 15 26 14 15 16 26 14 15 17 26 16 15 17 26 # 30 15 17 18 26 15 17 19 26 18 17 19 26 1 19 17 26 2 20 21 14 20 21 22 14 20 21 24 14 22 21 24 12 21 22 23 11 21 24 25 12 # 40 21 24 27 14 25 24 27 12 24 25 26 11 24 27 28 12 24 27 30 14 28 27 30 14 27 28 29 11 27 30 31 14 30 31 32 25 31 32 33 4 # 50 31 32 35 13 31 32 36 13 33 32 35 13 33 32 36 13 35 32 36 28 32 33 34 11 # improper dihedrals # NIDA 26 # IB JB KB LB MCB 5 4 7 6 1 7 5 9 8 1 9 7 11 10 1 4 5 7 9 1 5 7 9 11 1 7 9 11 3 1 4 3 11 9 1 11 3 4 5 1 3 4 5 7 1 11 9 12 3 1 # 10 11 2 4 3 1 2 3 11 12 1 2 1 13 12 1 13 12 14 1 1 1 2 19 13 1 13 14 15 17 1 14 15 17 19 1 15 17 19 1 1 13 1 19 17 1 19 1 13 14 1 # 20 1 13 14 15 1 15 14 17 16 1 17 15 19 18 1 21 22 24 20 2 24 25 27 21 2 27 28 30 24 2 # dihedrals # NDA 17 # IB JB KB LB MCB 3 11 12 13 4 11 12 13 1 4 13 1 2 3 4 1 2 3 11 4 1 2 20 21 20 2 20 21 24 17 20 21 22 23 12 20 21 24 27 17 21 24 25 26 12 21 24 27 30 17 # 10 24 27 28 29 12 24 27 30 31 17 27 30 31 32 14 30 31 32 33 11 30 31 32 33 9 31 32 33 34 11 31 32 33 34 9 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE FMNS # building block (residue, nucleotide, etc.) # RNME FMNS # number of atoms, number of preceding exclusions # NMAT NLIN 37 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 FC9A 11 12 0.20000 0 13 2 3 4 11 12 13 14 15 16 18 19 20 21 2 FN10 8 14 -0.20000 1 12 3 4 5 9 11 12 14 15 18 20 21 22 3 FC10A 11 12 0.36000 0 12 4 5 6 7 9 10 11 12 13 14 20 21 4 FN1 8 14 -0.36000 1 8 5 6 7 8 9 11 12 21 5 FC2 11 12 0.38000 0 6 6 7 8 9 10 11 6 FO2 1 16 -0.38000 1 3 7 8 9 7 FN3 8 14 -0.28000 0 5 8 9 10 11 12 8 FH3 18 1 0.28000 1 3 9 10 11 9 FC4 11 12 0.38000 0 5 10 11 12 13 14 10 FO4 1 16 -0.38000 1 2 11 12 11 FC4A 11 12 0.00000 1 5 12 13 14 15 21 12 FN5 8 14 -0.28000 0 5 13 14 15 16 20 13 FH5 18 1 0.28000 1 2 14 15 14 FC5A 11 12 0.00000 1 6 15 16 17 18 20 21 15 FC6 16 3 0.00000 1 5 16 17 18 19 20 16 FC7 11 12 0.00000 0 4 17 18 19 20 17 FCM7 14 5 0.00000 1 3 18 19 20 18 FC8 11 12 0.00000 0 2 19 20 19 FCM8 14 5 0.00000 1 1 20 20 FC9 16 3 0.00000 1 1 21 21 FCA 13 4 0.00000 1 3 22 23 25 22 FCB 12 3 0.15000 0 5 23 24 25 26 28 23 FOB 3 16 -0.54800 0 2 24 25 24 FHB 18 1 0.39800 1 0 25 FCG 12 3 0.15000 0 5 26 27 28 29 31 26 FOG 3 16 -0.54800 0 2 27 28 27 FHG 18 1 0.39800 1 0 28 FCD 12 3 0.15000 0 4 29 30 31 32 29 FOD 3 16 -0.54800 0 2 30 31 30 FHD 18 1 0.39800 1 0 31 FCE 13 4 0.15000 0 2 32 33 32 FOZ 3 16 -0.36000 0 5 33 34 35 36 37 33 FPH 27 31 1.08000 0 4 34 35 36 37 34 FOH 3 16 -0.54800 0 3 35 36 37 35 FHH 18 1 0.39800 0 2 36 37 36 FOT1 2 16 -0.36000 0 1 37 37 FOT2 2 16 -0.36000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 39 # IB JB MCB 1 2 16 1 14 15 1 20 15 2 3 16 2 21 22 3 4 11 3 11 15 4 5 11 5 6 4 5 7 16 # 10 7 8 2 7 9 16 9 10 4 9 11 15 11 12 16 12 13 2 12 14 16 14 15 15 15 16 15 16 17 26 # 20 16 18 15 18 19 26 18 20 15 21 22 26 22 23 17 22 25 26 23 24 1 25 26 17 25 28 26 26 27 1 # 30 28 29 17 28 31 26 29 30 1 31 32 17 32 33 27 33 34 27 33 36 23 33 37 23 34 35 1 # bond angles # NBA 58 # IB JB KB MCB 2 1 14 26 2 1 20 26 14 1 20 26 1 2 3 26 1 2 21 26 3 2 21 26 2 3 4 26 2 3 11 26 4 3 11 26 3 4 5 26 # 10 4 5 6 26 4 5 7 26 6 5 7 26 5 7 8 24 5 7 9 26 8 7 9 24 7 9 10 26 7 9 11 26 10 9 11 26 3 11 9 26 # 20 3 11 12 26 9 11 12 26 11 12 13 24 11 12 14 26 13 12 14 24 1 14 12 26 1 14 15 26 12 14 15 26 14 15 16 26 15 16 17 26 # 30 15 16 18 26 17 16 18 26 16 18 19 26 16 18 20 26 19 18 20 26 1 20 18 26 2 21 22 14 21 22 23 14 21 22 25 14 23 22 25 12 # 40 22 23 24 11 22 25 26 12 22 25 28 14 26 25 28 12 25 26 27 11 25 28 29 12 25 28 31 14 29 28 31 14 28 29 30 11 28 31 32 14 # 50 31 32 33 25 32 33 34 4 32 33 36 13 32 33 37 13 34 33 36 13 34 33 37 13 36 33 37 28 33 34 35 11 # improper dihedrals # NIDA 26 # IB JB KB LB MCB 5 4 7 6 1 7 5 9 8 1 9 7 11 10 1 4 5 7 9 1 5 7 9 11 1 7 9 11 3 1 4 3 11 9 1 11 3 4 5 1 3 4 5 7 1 11 9 12 3 1 # 10 11 2 4 3 1 2 3 11 12 1 2 1 14 12 1 14 12 15 1 1 1 2 20 14 1 14 15 16 18 1 15 16 18 20 1 16 18 20 1 1 14 1 20 18 1 20 1 14 15 1 # 20 1 14 15 16 1 16 15 18 17 1 18 16 20 19 1 22 23 25 21 2 25 26 28 22 2 28 29 31 25 2 # dihedrals # NDA 17 # IB JB KB LB MCB 3 11 12 14 4 11 12 14 1 4 14 1 2 3 4 1 2 3 11 4 1 2 21 22 20 2 21 22 25 17 21 22 23 24 12 21 22 25 28 17 22 25 26 27 12 22 25 28 31 17 # 10 25 28 29 30 12 25 28 31 32 17 28 31 32 33 14 31 32 33 34 11 31 32 33 34 9 32 33 34 35 11 32 33 34 35 9 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE FMNR # building block (residue, nucleotide, etc.) # RNME FMNR # number of atoms, number of preceding exclusions # NMAT NLIN 38 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 FC9A 11 12 0.10000 0 13 2 3 4 12 13 14 15 16 17 19 20 21 22 2 FN10 8 14 -0.20000 0 13 3 4 5 6 10 12 13 15 16 19 21 22 23 3 FC10A 11 12 0.10000 1 13 4 5 6 7 8 10 11 12 13 14 15 21 22 4 FN1 8 14 -0.28000 0 9 5 6 7 8 9 10 12 13 22 5 FH1 18 1 0.28000 1 4 6 7 8 12 6 FC2 11 12 0.38000 0 6 7 8 9 10 11 12 7 FO2 1 16 -0.38000 1 3 8 9 10 8 FN3 8 14 -0.28000 0 5 9 10 11 12 13 9 FH3 18 1 0.28000 1 3 10 11 12 10 FC4 11 12 0.38000 0 5 11 12 13 14 15 11 FO4 1 16 -0.38000 1 2 12 13 12 FC4A 11 12 0.00000 1 5 13 14 15 16 22 13 FN5 8 14 -0.28000 0 5 14 15 16 17 21 14 FH5 18 1 0.28000 1 2 15 16 15 FC5A 11 12 0.00000 1 6 16 17 18 19 21 22 16 FC6 16 3 0.00000 1 5 17 18 19 20 21 17 FC7 11 12 0.00000 0 4 18 19 20 21 18 FCM7 14 5 0.00000 1 3 19 20 21 19 FC8 11 12 0.00000 0 2 20 21 20 FCM8 14 5 0.00000 1 1 21 21 FC9 16 3 0.00000 1 1 22 22 FCA 13 4 0.00000 1 3 23 24 26 23 FCB 12 3 0.15000 0 5 24 25 26 27 29 24 FOB 3 16 -0.54800 0 2 25 26 25 FHB 18 1 0.39800 1 0 26 FCG 12 3 0.15000 0 5 27 28 29 30 32 27 FOG 3 16 -0.54800 0 2 28 29 28 FHG 18 1 0.39800 1 0 29 FCD 12 3 0.15000 0 4 30 31 32 33 30 FOD 3 16 -0.54800 0 2 31 32 31 FHD 18 1 0.39800 1 0 32 FCE 13 4 0.15000 0 2 33 34 33 FOZ 3 16 -0.36000 0 5 34 35 36 37 38 34 FPH 27 31 1.08000 0 4 35 36 37 38 35 FOH 3 16 -0.54800 0 3 36 37 38 36 FHH 18 1 0.39800 0 2 37 38 37 FOT1 2 16 -0.36000 0 1 38 38 FOT2 2 16 -0.36000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 40 # IB JB MCB 1 2 16 1 15 15 1 21 15 2 3 16 2 22 22 3 4 16 3 12 15 4 5 2 4 6 16 6 7 14 # 10 6 8 16 8 9 2 8 10 16 10 11 4 10 12 15 12 13 16 13 14 2 13 15 16 15 16 15 16 17 15 # 20 17 18 26 17 19 15 19 20 26 19 21 15 22 23 26 23 24 17 23 26 26 24 25 1 26 27 17 26 29 26 # 30 27 28 1 29 30 17 29 32 26 30 31 1 32 33 17 33 34 27 34 35 27 34 37 23 34 38 23 35 36 1 # 40 # bond angles # NBA 60 # IB JB KB MCB 2 1 15 26 2 1 21 26 15 1 21 26 1 2 3 26 1 2 22 26 3 2 22 26 2 3 4 26 2 3 12 26 4 3 12 26 3 4 5 24 # 10 3 4 6 26 5 4 6 24 4 6 7 26 4 6 8 26 7 6 8 26 6 8 9 24 6 8 10 26 9 8 10 24 8 10 11 26 8 10 12 26 # 20 11 10 12 26 3 12 10 26 3 12 13 26 10 12 13 26 12 13 14 24 12 13 15 26 14 13 15 24 1 15 13 26 1 15 16 26 13 15 16 26 # 30 15 16 17 26 16 17 18 26 16 17 19 26 18 17 19 26 17 19 20 26 17 19 21 26 20 19 21 26 1 21 19 26 2 22 23 14 22 23 24 14 # 40 22 23 26 14 24 23 26 12 23 24 25 11 23 26 27 12 23 26 29 14 27 26 29 12 26 27 28 11 26 29 30 12 26 29 32 14 30 29 32 14 # 50 29 30 31 11 29 32 33 14 32 33 34 25 33 34 35 4 33 34 37 13 33 34 38 13 35 34 37 13 35 34 38 13 37 34 38 28 34 35 36 11 # 60 # improper dihedrals # NIDA 27 # IB JB KB LB MCB 4 3 6 5 1 6 4 8 7 1 8 6 10 9 1 10 8 12 11 1 4 6 8 10 1 6 8 10 12 1 8 10 12 3 1 4 3 12 10 1 12 3 4 6 1 3 4 6 8 1 # 10 12 10 13 3 1 12 2 4 3 1 2 3 12 13 1 2 1 15 13 1 15 13 16 1 1 1 2 21 15 1 15 16 17 19 1 16 17 19 21 1 17 19 21 1 1 15 1 21 19 1 # 20 21 1 15 16 1 1 15 16 17 1 17 16 19 18 1 19 17 21 20 1 23 24 26 22 2 26 27 29 23 2 29 30 32 26 2 # dihedrals # NDA 17 # IB JB KB LB MCB 3 12 13 15 4 12 13 15 1 4 15 1 2 3 4 1 2 3 12 4 1 2 22 23 20 2 22 23 26 17 22 23 24 25 12 22 23 26 29 17 23 26 27 28 12 23 26 29 32 17 # 10 26 29 30 31 12 26 29 32 33 17 29 32 33 34 14 32 33 34 35 11 32 33 34 35 9 33 34 35 36 11 33 34 35 36 9 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE PFN # building block (residue, nucleotide, etc.) # RNME PFN # number of atoms, number of preceding exclusions # NMAT NLIN 21 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 FC9A 11 12 0.00000 0 11 2 3 4 11 12 13 14 15 16 20 21 2 FC10 16 3 0.00000 0 10 3 4 5 10 11 12 14 15 20 21 3 FC10A 11 12 0.00000 1 9 4 5 6 10 11 12 13 14 21 4 FC1 16 3 0.00000 0 6 5 6 7 10 11 12 5 FC2 16 3 0.00000 1 4 6 7 10 11 6 FC3 11 12 0.00000 1 6 7 8 9 10 11 12 7 FN3 6 14 -0.83000 0 4 8 9 10 11 8 FH31 18 1 0.41500 0 1 9 9 FH32 18 1 0.41500 1 0 10 FC4 16 3 0.00000 1 4 11 12 13 14 11 FC4A 11 12 0.00000 0 4 12 13 14 15 12 FN5 8 14 -0.36000 0 5 13 14 15 16 21 13 FH5 18 1 0.36000 0 2 14 15 14 FC5A 11 12 0.00000 1 5 15 16 17 20 21 15 FC6 16 3 0.00000 1 4 16 17 20 21 16 FC7 11 12 0.00000 1 5 17 18 19 20 21 17 FN7 6 14 -0.83000 0 4 18 19 20 21 18 FH71 18 1 0.41500 0 1 19 19 FH72 18 1 0.41500 1 0 20 FC8 16 3 0.00000 0 1 21 21 FC9 16 3 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 23 # IB JB MCB 1 2 15 1 14 15 1 21 15 2 3 15 3 4 15 3 11 15 4 5 15 5 6 15 6 7 8 6 10 15 # 10 7 8 2 7 9 2 10 11 15 11 12 16 12 13 2 12 14 16 14 15 15 15 16 15 16 17 8 16 20 15 # 20 17 18 2 17 19 2 20 21 15 # bond angles # NBA 34 # IB JB KB MCB 2 1 14 26 2 1 21 26 14 1 21 26 1 2 3 26 2 3 4 26 2 3 11 26 4 3 11 26 3 4 5 26 4 5 6 26 5 6 7 26 # 10 5 6 10 26 7 6 10 26 6 7 8 22 6 7 9 22 8 7 9 23 6 10 11 26 3 11 10 26 3 11 12 26 10 11 12 26 11 12 13 24 # 20 11 12 14 26 13 12 14 24 1 14 12 26 1 14 15 26 12 14 15 26 14 15 16 26 15 16 17 26 15 16 20 26 17 16 20 26 16 17 18 22 # 30 16 17 19 22 18 17 19 23 16 20 21 26 1 21 20 26 # improper dihedrals # NIDA 27 # IB JB KB LB MCB 1 2 3 11 1 2 3 11 12 1 3 11 12 14 1 11 12 14 1 1 2 1 14 12 1 14 1 2 3 1 12 11 14 13 1 11 2 4 3 1 11 10 12 3 1 11 3 4 5 1 # 10 3 4 5 6 1 4 5 6 10 1 5 6 10 11 1 6 10 11 3 1 4 3 11 10 1 6 5 10 7 1 7 8 9 6 1 14 12 15 1 1 1 2 21 14 1 14 15 16 20 1 # 20 15 16 20 21 1 16 20 21 1 1 14 1 21 20 1 21 1 14 15 1 1 14 15 16 1 17 15 20 16 1 17 18 19 16 1 # dihedrals # NDA 2 # IB JB KB LB MCB 5 6 7 8 4 20 16 17 18 4 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE NADP # building block (residue, nucleotide, etc.) # RNME NADP # number of atoms, number of preceding exclusions # NMAT NLIN 52 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 AP 27 31 1.21000 0 6 2 3 4 5 6 10 2 AO1P 2 16 -0.36000 0 3 3 4 5 3 AO2P 2 16 -0.36000 0 2 4 5 4 AO5* 3 16 -0.36000 1 3 5 10 11 5 O3P 3 16 -0.26000 0 4 6 7 8 9 6 NP 27 31 1.21000 0 4 7 8 9 32 7 NO1P 2 16 -0.36000 0 2 8 9 8 NO2P 2 16 -0.36000 0 1 9 9 NO5* 3 16 -0.36000 1 2 32 33 10 AC5* 13 4 0.00000 1 3 11 12 29 11 AC4* 12 3 0.16000 0 5 12 13 26 29 30 12 AO4* 3 16 -0.36000 0 4 13 14 26 29 13 AC1* 12 3 0.20000 1 9 14 15 16 23 24 25 26 27 29 14 AN9 8 14 -0.20000 0 8 15 16 17 19 23 24 25 26 15 AC4 11 12 0.20000 1 8 16 17 18 19 20 23 24 25 16 AN3 8 14 -0.36000 0 6 17 18 19 23 24 25 17 AC2 16 3 0.36000 1 4 18 19 20 23 18 AN1 8 14 -0.36000 0 4 19 20 23 24 19 AC6 11 12 0.36000 1 6 20 21 22 23 24 25 20 AN6 6 14 -0.83000 0 4 21 22 23 24 21 AH61 18 1 0.41500 0 1 22 22 AH62 18 1 0.41500 1 0 23 AC5 11 12 0.00000 0 2 24 25 24 AN7 8 14 -0.36000 0 1 25 25 AC8 16 3 0.36000 1 0 26 AC2* 12 3 0.15000 0 4 27 28 29 30 27 AO2* 3 16 -0.54800 0 2 28 29 28 AH2* 18 1 0.39800 1 0 29 AC3* 12 3 0.15000 0 2 30 31 30 AO3* 3 16 -0.54800 0 1 31 31 AH3* 18 1 0.39800 1 0 32 NC5* 13 4 0.00000 1 3 33 34 50 33 NC4* 12 3 0.16000 0 5 34 35 47 50 51 34 NO4* 3 16 -0.36000 0 4 35 36 47 50 35 NC1* 12 3 0.20000 1 8 36 37 38 39 41 47 48 50 36 NN1 8 14 -0.10000 0 7 37 38 39 40 41 42 47 37 NC6 16 3 0.10000 0 4 38 39 40 41 38 NC2 16 3 0.05000 0 4 39 40 41 42 39 NC3 11 12 0.00000 0 5 40 41 42 43 44 40 NC4 16 3 0.05000 0 2 41 42 41 NC5 16 3 -0.10000 1 1 42 42 NC7 11 12 0.38000 0 4 43 44 45 46 43 NO7 1 16 -0.38000 1 1 44 44 NN7 6 14 -0.83000 0 2 45 46 45 NH71 18 1 0.41500 0 1 46 46 NH72 18 1 0.41500 1 0 47 NC2* 12 3 0.15000 0 4 48 49 50 51 48 NO2* 3 16 -0.54800 0 2 49 50 49 NH2* 18 1 0.39800 1 0 50 NC3* 12 3 0.15000 0 2 51 52 51 NO3* 3 16 -0.54800 0 1 52 52 NH3* 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 56 # IB JB MCB 1 2 23 1 3 23 1 4 27 1 5 27 4 10 19 5 6 27 6 7 23 6 8 23 6 9 27 9 32 19 # 10 10 11 25 11 12 19 11 29 25 12 13 19 13 14 21 13 26 25 14 15 9 14 25 9 15 16 11 15 23 15 # 20 16 17 6 17 18 6 18 19 11 19 20 8 19 23 15 20 21 2 20 22 2 23 24 9 24 25 9 26 27 19 # 30 26 29 25 27 28 1 29 30 19 30 31 1 32 33 25 33 34 19 33 50 25 34 35 19 35 36 22 35 47 25 # 40 36 37 16 36 38 16 37 41 15 38 39 15 39 40 15 39 42 26 40 41 15 42 43 4 42 44 8 44 45 2 # 50 44 46 2 47 48 19 47 50 25 48 49 1 50 51 19 51 52 1 # bond angles # NBA 83 # IB JB KB MCB 2 1 3 28 2 1 4 13 2 1 5 13 3 1 4 13 3 1 5 13 4 1 5 4 1 4 10 25 1 5 6 25 5 6 7 13 5 6 8 13 # 10 5 6 9 4 7 6 8 28 7 6 9 13 8 6 9 13 6 9 32 25 4 10 11 8 10 11 12 8 10 11 29 7 12 11 29 8 11 12 13 9 # 20 12 13 14 8 12 13 26 8 14 13 26 8 13 14 15 36 13 14 25 36 15 14 25 6 14 15 16 38 14 15 23 6 16 15 23 26 15 16 17 26 # 30 16 17 18 26 17 18 19 26 18 19 20 26 18 19 23 26 20 19 23 26 19 20 21 22 19 20 22 22 21 20 22 23 15 23 19 26 15 23 24 6 # 40 19 23 24 38 23 24 25 6 14 25 24 6 13 26 27 8 13 26 29 7 27 26 29 8 26 27 28 11 11 29 26 7 11 29 30 8 26 29 30 8 # 50 29 30 31 11 9 32 33 8 32 33 34 8 32 33 50 7 34 33 50 8 33 34 35 9 34 35 36 8 34 35 47 8 36 35 47 7 35 36 37 26 # 60 35 36 38 26 37 36 38 26 36 37 41 26 36 38 39 26 38 39 40 26 38 39 42 26 40 39 42 26 39 40 41 26 37 41 40 26 39 42 43 29 # 70 39 42 44 18 43 42 44 32 42 44 45 22 42 44 46 22 45 44 46 23 35 47 48 8 35 47 50 7 48 47 50 8 47 48 49 11 33 50 47 7 # 80 33 50 51 8 47 50 51 8 50 51 52 11 # improper dihedrals # NIDA 34 # IB JB KB LB MCB 29 10 12 11 2 29 26 30 11 2 26 27 29 13 2 26 12 14 13 2 13 15 25 14 1 15 14 25 24 1 25 14 15 23 1 23 24 25 14 1 14 15 23 24 1 15 23 24 25 1 # 10 15 14 16 23 1 23 19 24 15 1 16 15 23 19 1 18 19 23 15 1 23 15 16 17 1 17 18 19 23 1 15 16 17 18 1 16 17 18 19 1 20 18 23 19 1 20 21 22 19 1 # 20 50 32 34 33 2 50 47 51 33 2 47 48 50 35 2 47 34 36 35 2 36 37 38 35 1 38 36 37 41 1 37 36 38 39 1 36 37 41 40 1 36 38 39 40 1 39 40 41 37 1 # 30 38 39 40 41 1 42 38 40 39 1 42 43 44 39 1 44 45 46 42 1 # dihedrals # NDA 53 # IB JB KB LB MCB 4 1 5 6 11 4 1 5 6 9 5 1 4 10 11 5 1 4 10 9 1 4 10 11 14 4 10 11 29 17 4 10 11 29 7 4 10 11 12 8 10 11 29 26 17 10 11 29 30 7 # 10 12 11 29 26 7 12 11 29 30 8 13 26 29 11 17 13 26 29 30 7 27 26 29 11 7 27 26 29 30 8 12 13 26 29 17 12 13 26 29 7 14 13 26 27 7 12 13 26 27 8 # 20 29 11 12 13 14 11 12 13 26 14 13 26 27 28 12 11 29 30 31 12 12 13 14 15 6 23 19 20 21 4 1 5 6 9 11 1 5 6 9 9 5 6 9 32 11 5 6 9 32 9 # 30 6 9 32 33 14 9 32 33 50 17 9 32 33 50 7 9 32 33 34 8 32 33 50 47 17 32 33 50 51 7 34 33 50 47 7 34 33 50 51 8 35 47 50 33 17 35 47 50 51 7 # 40 48 47 50 33 7 48 47 50 51 8 34 35 47 50 17 34 35 47 50 7 36 35 47 48 7 34 35 47 48 8 50 33 34 35 14 33 34 35 47 14 35 47 48 49 12 33 50 51 52 12 # 50 34 35 36 38 6 38 39 42 44 1 39 42 44 45 4 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE NADH # building block (residue, nucleotide, etc.) # RNME NADH # number of atoms, number of preceding exclusions # NMAT NLIN 52 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 AP 27 31 1.21000 0 6 2 3 4 5 6 10 2 AO1P 2 16 -0.36000 0 3 3 4 5 3 AO2P 2 16 -0.36000 0 2 4 5 4 AO5* 3 16 -0.36000 1 3 5 10 11 5 O3P 3 16 -0.26000 0 4 6 7 8 9 6 NP 27 31 1.21000 0 4 7 8 9 32 7 NO1P 2 16 -0.36000 0 2 8 9 8 NO2P 2 16 -0.36000 0 1 9 9 NO5* 3 16 -0.36000 1 2 32 33 10 AC5* 13 4 0.00000 1 3 11 12 29 11 AC4* 12 3 0.16000 0 5 12 13 26 29 30 12 AO4* 3 16 -0.36000 0 4 13 14 26 29 13 AC1* 12 3 0.20000 1 9 14 15 16 23 24 25 26 27 29 14 AN9 8 14 -0.20000 0 8 15 16 17 19 23 24 25 26 15 AC4 11 12 0.20000 1 8 16 17 18 19 20 23 24 25 16 AN3 8 14 -0.36000 0 6 17 18 19 23 24 25 17 AC2 16 3 0.36000 1 4 18 19 20 23 18 AN1 8 14 -0.36000 0 4 19 20 23 24 19 AC6 11 12 0.36000 1 6 20 21 22 23 24 25 20 AN6 6 14 -0.83000 0 4 21 22 23 24 21 AH61 18 1 0.41500 0 1 22 22 AH62 18 1 0.41500 1 0 23 AC5 11 12 0.00000 0 2 24 25 24 AN7 8 14 -0.36000 0 1 25 25 AC8 16 3 0.36000 1 0 26 AC2* 12 3 0.15000 0 4 27 28 29 30 27 AO2* 3 16 -0.54800 0 2 28 29 28 AH2* 18 1 0.39800 1 0 29 AC3* 12 3 0.15000 0 2 30 31 30 AO3* 3 16 -0.54800 0 1 31 31 AH3* 18 1 0.39800 1 0 32 NC5* 13 4 0.00000 1 3 33 34 50 33 NC4* 12 3 0.16000 0 5 34 35 47 50 51 34 NO4* 3 16 -0.36000 0 4 35 36 47 50 35 NC1* 12 3 0.20000 1 8 36 37 38 39 41 47 48 50 36 NN1 8 14 -0.20000 0 7 37 38 39 40 41 42 47 37 NC6 16 3 0.20000 0 4 38 39 40 41 38 NC2 16 3 0.00000 0 4 39 40 41 42 39 NC3 11 12 0.00000 0 5 40 41 42 43 44 40 NC4 13 4 0.00000 0 2 41 42 41 NC5 16 3 0.00000 1 1 42 42 NC7 11 12 0.38000 0 4 43 44 45 46 43 NO7 1 16 -0.38000 1 1 44 44 NN7 6 14 -0.83000 0 2 45 46 45 NH71 18 1 0.41500 0 1 46 46 NH72 18 1 0.41500 1 0 47 NC2* 12 3 0.15000 0 4 48 49 50 51 48 NO2* 3 16 -0.54800 0 2 49 50 49 NH2* 18 1 0.39800 1 0 50 NC3* 12 3 0.15000 0 2 51 52 51 NO3* 3 16 -0.54800 0 1 52 52 NH3* 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 56 # IB JB MCB 1 2 23 1 3 23 1 4 27 1 5 27 4 10 19 5 6 27 6 7 23 6 8 23 6 9 27 9 32 19 # 10 10 11 25 11 12 19 11 29 25 12 13 19 13 14 21 13 26 25 14 15 9 14 25 9 15 16 11 15 23 15 # 20 16 17 6 17 18 6 18 19 11 19 20 8 19 23 15 20 21 2 20 22 2 23 24 9 24 25 9 26 27 19 # 30 26 29 25 27 28 1 29 30 19 30 31 1 32 33 25 33 34 19 33 50 25 34 35 19 35 36 22 35 47 25 # 40 36 37 16 36 38 16 37 41 15 38 39 15 39 40 14 39 42 26 40 41 14 42 43 4 42 44 8 44 45 2 # 50 44 46 2 47 48 19 47 50 25 48 49 1 50 51 19 51 52 1 # bond angles # NBA 83 # IB JB KB MCB 2 1 3 28 2 1 4 13 2 1 5 13 3 1 4 13 3 1 5 13 4 1 5 4 1 4 10 25 1 5 6 25 5 6 7 13 5 6 8 13 # 10 5 6 9 4 7 6 8 28 7 6 9 13 8 6 9 13 6 9 32 25 4 10 11 8 10 11 12 8 10 11 29 7 12 11 29 8 11 12 13 9 # 20 12 13 14 8 12 13 26 8 14 13 26 8 13 14 15 36 13 14 25 36 15 14 25 6 14 15 16 38 14 15 23 6 16 15 23 26 15 16 17 26 # 30 16 17 18 26 17 18 19 26 18 19 20 26 18 19 23 26 20 19 23 26 19 20 21 22 19 20 22 22 21 20 22 23 15 23 19 26 15 23 24 6 # 40 19 23 24 38 23 24 25 6 14 25 24 6 13 26 27 8 13 26 29 7 27 26 29 8 26 27 28 11 11 29 26 7 11 29 30 8 26 29 30 8 # 50 29 30 31 11 9 32 33 8 32 33 34 8 32 33 50 7 34 33 50 8 33 34 35 9 34 35 36 8 34 35 47 8 36 35 47 7 35 36 37 26 # 60 35 36 38 26 37 36 38 26 36 37 41 26 36 38 39 26 38 39 40 26 38 39 42 26 40 39 42 26 39 40 41 26 37 41 40 26 39 42 43 29 # 70 39 42 44 18 43 42 44 32 42 44 45 22 42 44 46 22 45 44 46 23 35 47 48 8 35 47 50 7 48 47 50 8 47 48 49 11 33 50 47 7 # 80 33 50 51 8 47 50 51 8 50 51 52 11 # improper dihedrals # NIDA 34 # IB JB KB LB MCB 29 10 12 11 2 29 26 30 11 2 26 27 29 13 2 26 12 14 13 2 13 15 25 14 1 15 14 25 24 1 25 14 15 23 1 23 24 25 14 1 14 15 23 24 1 15 23 24 25 1 # 10 15 14 16 23 1 23 19 24 15 1 16 15 23 19 1 18 19 23 15 1 23 15 16 17 1 17 18 19 23 1 15 16 17 18 1 16 17 18 19 1 20 18 23 19 1 20 21 22 19 1 # 20 50 32 34 33 2 50 47 51 33 2 47 48 50 35 2 47 34 36 35 2 36 37 38 35 1 38 36 37 41 1 37 36 38 39 1 36 37 41 40 1 36 38 39 40 1 39 40 41 37 1 # 30 38 39 40 41 1 42 38 40 39 1 42 43 44 39 1 44 45 46 42 1 # dihedrals # NDA 53 # IB JB KB LB MCB 4 1 5 6 11 4 1 5 6 9 5 1 4 10 11 5 1 4 10 9 1 4 10 11 14 4 10 11 29 17 4 10 11 29 7 4 10 11 12 8 10 11 29 26 17 10 11 29 30 7 # 10 12 11 29 26 7 12 11 29 30 8 13 26 29 11 17 13 26 29 30 7 27 26 29 11 7 27 26 29 30 8 12 13 26 29 17 12 13 26 29 7 14 13 26 27 7 12 13 26 27 8 # 20 29 11 12 13 14 11 12 13 26 14 13 26 27 28 12 11 29 30 31 12 12 13 14 15 6 23 19 20 21 4 1 5 6 9 11 1 5 6 9 9 5 6 9 32 11 5 6 9 32 9 # 30 6 9 32 33 14 9 32 33 50 17 9 32 33 50 7 9 32 33 34 8 32 33 50 47 17 32 33 50 51 7 34 33 50 47 7 34 33 50 51 8 35 47 50 33 17 35 47 50 51 7 # 40 48 47 50 33 7 48 47 50 51 8 34 35 47 50 17 34 35 47 50 7 36 35 47 48 7 34 35 47 48 8 50 33 34 35 14 33 34 35 47 14 35 47 48 49 12 33 50 51 52 12 # 50 34 35 36 38 6 38 39 42 44 1 39 42 44 45 4 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE NDPH # building block (residue, nucleotide, etc.) # RNME NDPH # number of atoms, number of preceding exclusions # NMAT NLIN 56 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 AP 27 31 1.21000 0 6 2 3 4 5 6 10 2 AO1P 2 16 -0.36000 0 3 3 4 5 3 AO2P 2 16 -0.36000 0 2 4 5 4 AO5* 3 16 -0.36000 1 3 5 10 11 5 O3P 3 16 -0.26000 0 4 6 7 8 9 6 NP 27 31 1.21000 0 4 7 8 9 36 7 NO1P 2 16 -0.36000 0 2 8 9 8 NO2P 2 16 -0.36000 0 1 9 9 NO5* 3 16 -0.36000 1 2 36 37 10 AC5* 13 4 0.00000 1 3 11 12 33 11 AC4* 12 3 0.16000 0 5 12 13 26 33 34 12 AO4* 3 16 -0.36000 0 4 13 14 26 33 13 AC1* 12 3 0.20000 1 9 14 15 16 23 24 25 26 27 33 14 AN9 8 14 -0.20000 0 8 15 16 17 19 23 24 25 26 15 AC4 11 12 0.20000 1 8 16 17 18 19 20 23 24 25 16 AN3 8 14 -0.36000 0 6 17 18 19 23 24 25 17 AC2 16 3 0.36000 1 4 18 19 20 23 18 AN1 8 14 -0.36000 0 4 19 20 23 24 19 AC6 11 12 0.36000 1 6 20 21 22 23 24 25 20 AN6 6 14 -0.83000 0 4 21 22 23 24 21 AH61 18 1 0.41500 0 1 22 22 AH62 18 1 0.41500 1 0 23 AC5 11 12 0.00000 0 2 24 25 24 AN7 8 14 -0.36000 0 1 25 25 AC8 16 3 0.36000 1 0 26 AC2* 12 3 0.15000 0 4 27 28 33 34 27 AO2* 3 16 -0.36000 0 6 28 29 30 31 32 33 28 AP2* 27 31 1.08000 0 4 29 30 31 32 29 AO6* 2 16 -0.36000 0 3 30 31 32 30 AO7* 2 16 -0.36000 0 2 31 32 31 AO8* 3 16 -0.54800 0 1 32 32 AH8* 18 1 0.39800 1 0 33 AC3* 12 3 0.15000 0 2 34 35 34 AO3* 3 16 -0.54800 0 1 35 35 AH3* 18 1 0.39800 1 0 36 NC5* 13 4 0.00000 1 3 37 38 54 37 NC4* 12 3 0.16000 0 5 38 39 51 54 55 38 NO4* 3 16 -0.36000 0 4 39 40 51 54 39 NC1* 12 3 0.20000 1 8 40 41 42 43 45 51 52 54 40 NN1 8 14 -0.20000 0 7 41 42 43 44 45 46 51 41 NC6 16 3 0.20000 0 4 42 43 44 45 42 NC2 16 3 0.00000 0 4 43 44 45 46 43 NC3 11 12 0.00000 0 5 44 45 46 47 48 44 NC4 13 4 0.00000 0 2 45 46 45 NC5 16 3 0.00000 1 1 46 46 NC7 11 12 0.38000 0 4 47 48 49 50 47 NO7 1 16 -0.38000 1 1 48 48 NN7 6 14 -0.83000 0 2 49 50 49 NH71 18 1 0.41500 0 1 50 50 NH72 18 1 0.41500 1 0 51 NC2* 12 3 0.15000 0 4 52 53 54 55 52 NO2* 3 16 -0.54800 0 2 53 54 53 NH2* 18 1 0.39800 1 0 54 NC3* 12 3 0.15000 0 2 55 56 55 NO3* 3 16 -0.54800 0 1 56 56 NH3* 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 60 # IB JB MCB 1 2 23 1 3 23 1 4 27 1 5 27 4 10 19 5 6 27 6 7 23 6 8 23 6 9 27 9 36 19 # 10 10 11 25 11 12 19 11 33 25 12 13 19 13 14 21 13 26 25 14 15 9 14 25 9 15 16 11 15 23 15 # 20 16 17 6 17 18 6 18 19 11 19 20 8 19 23 15 20 21 2 20 22 2 23 24 9 24 25 9 26 27 19 # 30 26 33 25 27 28 27 28 29 23 28 30 23 28 31 27 31 32 1 33 34 19 34 35 1 36 37 25 37 38 19 # 40 37 54 25 38 39 19 39 40 22 39 51 25 40 41 16 40 42 16 41 45 15 42 43 15 43 44 14 43 46 26 # 50 44 45 14 46 47 4 46 48 8 48 49 2 48 50 2 51 52 19 51 54 25 52 53 1 54 55 19 55 56 1 # 60 # bond angles # NBA 90 # IB JB KB MCB 2 1 3 28 2 1 4 13 2 1 5 13 3 1 4 13 3 1 5 13 4 1 5 4 1 4 10 25 1 5 6 25 5 6 7 13 5 6 8 13 # 10 5 6 9 4 7 6 8 28 7 6 9 13 8 6 9 13 6 9 36 25 4 10 11 8 10 11 12 8 10 11 33 7 12 11 33 8 11 12 13 9 # 20 12 13 14 8 12 13 26 8 14 13 26 8 13 14 15 36 13 14 25 36 15 14 25 6 14 15 16 38 14 15 23 6 16 15 23 26 15 16 17 26 # 30 16 17 18 26 17 18 19 26 18 19 20 26 18 19 23 26 20 19 23 26 19 20 21 22 19 20 22 22 21 20 22 23 15 23 19 26 15 23 24 6 # 40 19 23 24 38 23 24 25 6 14 25 24 6 13 26 27 8 13 26 33 7 27 26 33 8 26 27 28 25 27 28 29 13 27 28 30 13 27 28 31 4 # 50 29 28 30 28 29 28 31 13 30 28 31 13 28 31 32 11 11 33 26 7 11 33 34 8 26 33 34 8 33 34 35 11 9 36 37 8 36 37 38 8 # 60 36 37 54 7 38 37 54 8 37 38 39 9 38 39 40 8 38 39 51 8 40 39 51 7 39 40 41 26 39 40 42 26 41 40 42 26 40 41 45 26 # 70 40 42 43 26 42 43 44 26 42 43 46 26 44 43 46 26 43 44 45 26 41 45 44 26 43 46 47 29 43 46 48 18 47 46 48 32 46 48 49 22 # 80 46 48 50 22 49 48 50 23 39 51 52 8 39 51 54 7 52 51 54 8 51 52 53 11 37 54 51 7 37 54 55 8 51 54 55 8 54 55 56 11 # 90 # improper dihedrals # NIDA 34 # IB JB KB LB MCB 33 10 12 11 2 33 26 34 11 2 26 27 33 13 2 26 12 14 13 2 13 15 25 14 1 15 14 25 24 1 25 14 15 23 1 23 24 25 14 1 14 15 23 24 1 15 23 24 25 1 # 10 15 14 16 23 1 23 19 24 15 1 16 15 23 19 1 18 19 23 15 1 23 15 16 17 1 17 18 19 23 1 15 16 17 18 1 16 17 18 19 1 20 18 23 19 1 20 21 22 19 1 # 20 54 36 38 37 2 54 51 55 37 2 51 52 54 39 2 51 38 40 39 2 40 41 42 39 1 42 40 41 45 1 41 40 42 43 1 40 41 45 44 1 40 42 43 44 1 43 44 45 41 1 # 30 42 43 44 45 1 46 42 44 43 1 46 47 48 43 1 48 49 50 46 1 # dihedrals # NDA 57 # IB JB KB LB MCB 4 1 5 6 11 4 1 5 6 9 5 1 4 10 11 5 1 4 10 9 1 4 10 11 14 4 10 11 33 17 4 10 11 33 7 4 10 11 12 8 10 11 33 26 17 10 11 33 34 7 # 10 12 11 33 26 7 12 11 33 34 8 13 26 33 11 17 13 26 33 34 7 27 26 33 11 7 27 26 33 34 8 12 13 26 33 17 12 13 26 33 7 14 13 26 27 7 12 13 26 27 8 # 20 33 11 12 13 14 11 12 13 26 14 13 26 27 28 12 26 27 28 31 11 26 27 28 31 9 27 28 31 32 11 27 28 31 32 9 11 33 34 35 12 12 13 14 15 6 23 19 20 21 4 # 30 1 5 6 9 11 1 5 6 9 9 5 6 9 36 11 5 6 9 36 9 6 9 36 37 14 9 36 37 54 17 9 36 37 54 7 9 36 37 38 8 36 37 54 51 17 36 37 54 55 7 # 40 38 37 54 51 7 38 37 54 55 8 39 51 54 37 17 39 51 54 55 7 52 51 54 37 7 52 51 54 55 8 38 39 51 54 17 38 39 51 54 7 40 39 51 52 7 38 39 51 52 8 # 50 54 37 38 39 14 37 38 39 51 14 39 51 52 53 12 37 54 55 56 12 38 39 40 42 6 42 43 46 48 1 43 46 48 49 4 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE NDPP # building block (residue, nucleotide, etc.) # RNME NDPP # number of atoms, number of preceding exclusions # NMAT NLIN 56 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 AP 27 31 1.21000 0 6 2 3 4 5 6 10 2 AO1P 2 16 -0.36000 0 3 3 4 5 3 AO2P 2 16 -0.36000 0 2 4 5 4 AO5* 3 16 -0.36000 1 3 5 10 11 5 O3P 3 16 -0.26000 0 4 6 7 8 9 6 NP 27 31 1.21000 0 4 7 8 9 36 7 NO1P 2 16 -0.36000 0 2 8 9 8 NO2P 2 16 -0.36000 0 1 9 9 NO5* 3 16 -0.36000 1 2 36 37 10 AC5* 13 4 0.00000 1 3 11 12 33 11 AC4* 12 3 0.16000 0 5 12 13 26 33 34 12 AO4* 3 16 -0.36000 0 4 13 14 26 33 13 AC1* 12 3 0.20000 1 9 14 15 16 23 24 25 26 27 33 14 AN9 8 14 -0.20000 0 8 15 16 17 19 23 24 25 26 15 AC4 11 12 0.20000 1 8 16 17 18 19 20 23 24 25 16 AN3 8 14 -0.36000 0 6 17 18 19 23 24 25 17 AC2 16 3 0.36000 1 4 18 19 20 23 18 AN1 8 14 -0.36000 0 4 19 20 23 24 19 AC6 11 12 0.36000 1 6 20 21 22 23 24 25 20 AN6 6 14 -0.83000 0 4 21 22 23 24 21 AH61 18 1 0.41500 0 1 22 22 AH62 18 1 0.41500 1 0 23 AC5 11 12 0.00000 0 2 24 25 24 AN7 8 14 -0.36000 0 1 25 25 AC8 16 3 0.36000 1 0 26 AC2* 12 3 0.15000 0 4 27 28 33 34 27 AO2* 3 16 -0.36000 0 6 28 29 30 31 32 33 28 AP2* 27 31 1.08000 0 4 29 30 31 32 29 AO6* 2 16 -0.36000 0 3 30 31 32 30 AO7* 2 16 -0.36000 0 2 31 32 31 AO8* 3 16 -0.54800 0 1 32 32 AH8* 18 1 0.39800 1 0 33 AC3* 12 3 0.15000 0 2 34 35 34 AO3* 3 16 -0.54800 0 1 35 35 AH3* 18 1 0.39800 1 0 36 NC5* 13 4 0.00000 1 3 37 38 54 37 NC4* 12 3 0.16000 0 5 38 39 51 54 55 38 NO4* 3 16 -0.36000 0 4 39 40 51 54 39 NC1* 12 3 0.20000 1 8 40 41 42 43 45 51 52 54 40 NN1 8 14 -0.10000 0 7 41 42 43 44 45 46 51 41 NC6 16 3 0.10000 0 4 42 43 44 45 42 NC2 16 3 0.05000 0 4 43 44 45 46 43 NC3 11 12 0.00000 0 5 44 45 46 47 48 44 NC4 16 3 0.05000 0 2 45 46 45 NC5 16 3 -0.10000 1 1 46 46 NC7 11 12 0.38000 0 4 47 48 49 50 47 NO7 1 16 -0.38000 1 1 48 48 NN7 6 14 -0.83000 0 2 49 50 49 NH71 18 1 0.41500 0 1 50 50 NH72 18 1 0.41500 1 0 51 NC2* 12 3 0.15000 0 4 52 53 54 55 52 NO2* 3 16 -0.54800 0 2 53 54 53 NH2* 18 1 0.39800 1 0 54 NC3* 12 3 0.15000 0 2 55 56 55 NO3* 3 16 -0.54800 0 1 56 56 NH3* 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 60 # IB JB MCB 1 2 23 1 3 23 1 4 27 1 5 27 4 10 19 5 6 27 6 7 23 6 8 23 6 9 27 9 36 19 # 10 10 11 25 11 12 19 11 33 25 12 13 19 13 14 21 13 26 25 14 15 9 14 25 9 15 16 11 15 23 15 # 20 16 17 6 17 18 6 18 19 11 19 20 8 19 23 15 20 21 2 20 22 2 23 24 9 24 25 9 26 27 19 # 30 26 33 25 27 28 27 28 29 23 28 30 23 28 31 27 31 32 1 33 34 19 34 35 1 36 37 25 37 38 19 # 40 37 54 25 38 39 19 39 40 22 39 51 25 40 41 16 40 42 16 41 45 15 42 43 15 43 44 15 43 46 26 # 50 44 45 15 46 47 4 46 48 8 48 49 2 48 50 2 51 52 19 51 54 25 52 53 1 54 55 19 55 56 1 # 60 # bond angles # NBA 90 # IB JB KB MCB 2 1 3 28 2 1 4 13 2 1 5 13 3 1 4 13 3 1 5 13 4 1 5 4 1 4 10 25 1 5 6 25 5 6 7 13 5 6 8 13 # 10 5 6 9 4 7 6 8 28 7 6 9 13 8 6 9 13 6 9 36 25 4 10 11 8 10 11 12 8 10 11 33 7 12 11 33 8 11 12 13 9 # 20 12 13 14 8 12 13 26 8 14 13 26 8 13 14 15 36 13 14 25 36 15 14 25 6 14 15 16 38 14 15 23 6 16 15 23 26 15 16 17 26 # 30 16 17 18 26 17 18 19 26 18 19 20 26 18 19 23 26 20 19 23 26 19 20 21 22 19 20 22 22 21 20 22 23 15 23 19 26 15 23 24 6 # 40 19 23 24 38 23 24 25 6 14 25 24 6 13 26 27 8 13 26 33 7 27 26 33 8 26 27 28 25 27 28 29 13 27 28 30 13 27 28 31 4 # 50 29 28 30 28 29 28 31 13 30 28 31 13 28 31 32 11 11 33 26 7 11 33 34 8 26 33 34 8 33 34 35 11 9 36 37 8 36 37 38 8 # 60 36 37 54 7 38 37 54 8 37 38 39 9 38 39 40 8 38 39 51 8 40 39 51 7 39 40 41 26 39 40 42 26 41 40 42 26 40 41 45 26 # 70 40 42 43 26 42 43 44 26 42 43 46 26 44 43 46 26 43 44 45 26 41 45 44 26 43 46 47 29 43 46 48 18 47 46 48 32 46 48 49 22 # 80 46 48 50 22 49 48 50 23 39 51 52 8 39 51 54 7 52 51 54 8 51 52 53 11 37 54 51 7 37 54 55 8 51 54 55 8 54 55 56 11 # 90 # improper dihedrals # NIDA 34 # IB JB KB LB MCB 33 10 12 11 2 33 26 34 11 2 26 27 33 13 2 26 12 14 13 2 13 15 25 14 1 15 14 25 24 1 25 14 15 23 1 23 24 25 14 1 14 15 23 24 1 15 23 24 25 1 # 10 15 14 16 23 1 23 19 24 15 1 16 15 23 19 1 18 19 23 15 1 23 15 16 17 1 17 18 19 23 1 15 16 17 18 1 16 17 18 19 1 20 18 23 19 1 20 21 22 19 1 # 20 54 36 38 37 2 54 51 55 37 2 51 52 54 39 2 51 38 40 39 2 40 41 42 39 1 42 40 41 45 1 41 40 42 43 1 40 41 45 44 1 40 42 43 44 1 43 44 45 41 1 # 30 42 43 44 45 1 46 42 44 43 1 46 47 48 43 1 48 49 50 46 1 # dihedrals # NDA 57 # IB JB KB LB MCB 4 1 5 6 11 4 1 5 6 9 5 1 4 10 11 5 1 4 10 9 1 4 10 11 14 4 10 11 33 17 4 10 11 33 7 4 10 11 12 8 10 11 33 26 17 10 11 33 34 7 # 10 12 11 33 26 7 12 11 33 34 8 13 26 33 11 17 13 26 33 34 7 27 26 33 11 7 27 26 33 34 8 12 13 26 33 17 12 13 26 33 7 14 13 26 27 7 12 13 26 27 8 # 20 33 11 12 13 14 11 12 13 26 14 13 26 27 28 12 26 27 28 31 11 26 27 28 31 9 27 28 31 32 11 27 28 31 32 9 11 33 34 35 12 12 13 14 15 6 23 19 20 21 4 # 30 1 5 6 9 11 1 5 6 9 9 5 6 9 36 11 5 6 9 36 9 6 9 36 37 14 9 36 37 54 17 9 36 37 54 7 9 36 37 38 8 36 37 54 51 17 36 37 54 55 7 # 40 38 37 54 51 7 38 37 54 55 8 39 51 54 37 17 39 51 54 55 7 52 51 54 37 7 52 51 54 55 8 38 39 51 54 17 38 39 51 54 7 40 39 51 52 7 38 39 51 52 8 # 50 54 37 38 39 14 37 38 39 51 14 39 51 52 53 12 37 54 55 56 12 38 39 40 42 6 42 43 46 48 1 43 46 48 49 4 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE NDPHN # building block (residue, nucleotide, etc.) # RNME NDPHN # number of atoms, number of preceding exclusions # NMAT NLIN 59 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 AP 27 31 1.02000 0 7 2 3 4 5 6 7 12 2 AO1P 3 16 -0.54800 0 4 3 4 5 6 3 AH1P 18 1 0.39800 0 3 4 5 6 4 AO2P 1 16 -0.38000 0 2 5 6 5 AO5* 3 16 -0.36000 1 3 6 12 13 6 O3P 3 16 -0.26000 0 5 7 8 9 10 11 7 NP 27 31 1.02000 0 5 8 9 10 11 39 8 NO1P 3 16 -0.54800 0 3 9 10 11 9 NH1P 18 1 0.39800 0 2 10 11 10 NO2P 1 16 -0.38000 0 1 11 11 NO5* 3 16 -0.36000 1 2 39 40 12 AC5* 13 4 0.00000 1 3 13 14 36 13 AC4* 12 3 0.16000 0 5 14 15 28 36 37 14 AO4* 3 16 -0.36000 0 4 15 16 28 36 15 AC1* 12 3 0.20000 1 9 16 17 18 25 26 27 28 29 36 16 AN9 8 14 -0.20000 0 8 17 18 19 21 25 26 27 28 17 AC4 11 12 0.20000 1 8 18 19 20 21 22 25 26 27 18 AN3 8 14 -0.36000 0 6 19 20 21 25 26 27 19 AC2 16 3 0.36000 1 4 20 21 22 25 20 AN1 8 14 -0.36000 0 4 21 22 25 26 21 AC6 11 12 0.36000 1 6 22 23 24 25 26 27 22 AN6 6 14 -0.83000 0 4 23 24 25 26 23 AH61 18 1 0.41500 0 1 24 24 AH62 18 1 0.41500 1 0 25 AC5 11 12 0.00000 0 2 26 27 26 AN7 8 14 -0.36000 0 1 27 27 AC8 16 3 0.36000 1 0 28 AC2* 12 3 0.15000 0 4 29 30 36 37 29 AO2* 3 16 -0.36000 0 7 30 31 32 33 34 35 36 30 AP2* 27 31 0.89000 0 5 31 32 33 34 35 31 AO6* 1 16 -0.38000 0 4 32 33 34 35 32 AO7* 3 16 -0.54800 0 3 33 34 35 33 AH7* 18 1 0.39800 0 2 34 35 34 AO8* 3 16 -0.54800 0 1 35 35 AH8* 18 1 0.39800 1 0 36 AC3* 12 3 0.15000 0 2 37 38 37 AO3* 3 16 -0.54800 0 1 38 38 AH3* 18 1 0.39800 1 0 39 NC5* 13 4 0.00000 1 3 40 41 57 40 NC4* 12 3 0.16000 0 5 41 42 54 57 58 41 NO4* 3 16 -0.36000 0 4 42 43 54 57 42 NC1* 12 3 0.20000 1 8 43 44 45 46 48 54 55 57 43 NN1 8 14 -0.20000 0 7 44 45 46 47 48 49 54 44 NC6 16 3 0.20000 0 4 45 46 47 48 45 NC2 16 3 0.00000 0 4 46 47 48 49 46 NC3 11 12 0.00000 0 5 47 48 49 50 51 47 NC4 13 4 0.00000 0 2 48 49 48 NC5 16 3 0.00000 1 1 49 49 NC7 11 12 0.38000 0 4 50 51 52 53 50 NO7 1 16 -0.38000 1 1 51 51 NN7 6 14 -0.83000 0 2 52 53 52 NH71 18 1 0.41500 0 1 53 53 NH72 18 1 0.41500 1 0 54 NC2* 12 3 0.15000 0 4 55 56 57 58 55 NO2* 3 16 -0.54800 0 2 56 57 56 NH2* 18 1 0.39800 1 0 57 NC3* 12 3 0.15000 0 2 58 59 58 NO3* 3 16 -0.54800 0 1 59 59 NH3* 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 63 # IB JB MCB 1 2 27 2 3 1 1 4 23 1 5 27 1 6 27 5 12 19 6 7 27 7 8 27 8 9 1 7 10 23 # 10 7 11 27 11 39 19 12 13 25 13 14 19 13 36 25 14 15 19 15 16 21 15 28 25 16 17 9 16 27 9 # 20 17 18 11 17 25 15 18 19 6 19 20 6 20 21 11 21 22 8 21 25 15 22 23 2 22 24 2 25 26 9 # 30 26 27 9 28 29 19 28 36 25 29 30 27 30 31 23 30 32 27 30 34 27 32 33 1 34 35 1 36 37 19 # 40 37 38 1 39 40 25 40 41 19 40 57 25 41 42 19 42 43 22 42 54 25 43 44 16 43 45 16 44 48 15 # 50 45 46 15 46 47 14 46 49 26 47 48 14 49 50 4 49 51 8 51 52 2 51 53 2 54 55 19 54 57 25 # 60 55 56 1 57 58 19 58 59 1 # bond angles # NBA 93 # IB JB KB MCB 1 2 3 11 2 1 4 13 2 1 5 13 2 1 6 13 4 1 5 13 4 1 6 13 5 1 6 13 1 5 12 25 1 6 7 25 6 7 8 13 # 10 6 7 10 13 6 7 11 13 8 7 10 13 8 7 11 13 10 7 11 13 7 8 9 11 7 11 39 25 5 12 13 8 12 13 14 8 12 13 36 7 # 20 14 13 36 8 13 14 15 9 14 15 16 8 14 15 28 8 16 15 28 8 15 16 17 36 15 16 27 36 17 16 27 6 16 17 18 38 16 17 25 6 # 30 18 17 25 26 17 18 19 26 18 19 20 26 19 20 21 26 20 21 22 26 20 21 25 26 22 21 25 26 21 22 23 22 21 22 24 22 23 22 24 23 # 40 17 25 21 26 17 25 26 6 21 25 26 38 25 26 27 6 16 27 26 6 15 28 29 8 15 28 36 7 29 28 36 8 28 29 30 25 29 30 31 13 # 50 29 30 32 13 29 30 34 13 31 30 32 13 31 30 34 13 32 30 34 13 30 32 33 11 30 34 35 11 13 36 28 7 13 36 37 8 28 36 37 8 # 60 36 37 38 11 11 39 40 8 39 40 41 8 39 40 57 7 41 40 57 8 40 41 42 9 41 42 43 8 41 42 54 8 43 42 54 7 42 43 44 26 # 70 42 43 45 26 44 43 45 26 43 44 48 26 43 45 46 26 45 46 47 26 45 46 49 26 47 46 49 26 46 47 48 26 44 48 47 26 46 49 50 29 # 80 46 49 51 18 50 49 51 32 49 51 52 22 49 51 53 22 52 51 53 23 42 54 55 8 42 54 57 7 55 54 57 8 54 55 56 11 40 57 54 7 # 90 40 57 58 8 54 57 58 8 57 58 59 11 # improper dihedrals # NIDA 34 # IB JB KB LB MCB 36 12 14 13 2 36 28 37 13 2 28 29 36 15 2 28 14 16 15 2 15 17 27 16 1 17 16 27 26 1 27 16 17 25 1 25 26 27 16 1 16 17 25 26 1 17 25 26 27 1 # 10 17 16 18 25 1 25 21 26 17 1 18 17 25 21 1 20 21 25 17 1 25 17 18 19 1 19 20 21 25 1 17 18 19 20 1 18 19 20 21 1 22 20 25 21 1 22 23 24 21 1 # 20 57 39 41 40 2 57 54 58 40 2 54 55 57 42 2 54 41 43 42 2 43 44 45 42 1 45 43 44 48 1 44 43 45 46 1 43 44 48 47 1 43 45 46 47 1 46 47 48 44 1 # 30 45 46 47 48 1 49 45 47 46 1 49 50 51 46 1 51 52 53 49 1 # dihedrals # NDA 63 # IB JB KB LB MCB 5 1 2 3 11 5 1 2 3 9 5 1 6 7 11 5 1 6 7 9 6 1 5 12 11 6 1 5 12 9 1 5 12 13 14 5 12 13 36 17 5 12 13 36 7 5 12 13 14 8 # 10 12 13 36 28 17 12 13 36 37 7 14 13 36 28 7 14 13 36 37 8 15 28 36 13 17 15 28 36 37 7 29 28 36 13 7 29 28 36 37 8 14 15 28 36 17 14 15 28 36 7 # 20 16 15 28 29 7 14 15 28 29 8 36 13 14 15 14 13 14 15 28 14 15 28 29 30 12 28 29 30 34 11 28 29 30 34 9 29 30 34 35 11 29 30 34 35 9 29 30 32 33 11 # 30 29 30 32 33 9 13 36 37 38 12 14 15 16 17 6 25 21 22 23 4 1 6 7 11 11 1 6 7 11 9 6 7 11 39 11 6 7 11 39 9 11 7 8 9 11 11 7 8 9 9 # 40 7 11 39 40 14 11 39 40 57 17 11 39 40 57 7 11 39 40 41 8 39 40 57 54 17 39 40 57 58 7 41 40 57 54 7 41 40 57 58 8 42 54 57 40 17 42 54 57 58 7 # 50 55 54 57 40 7 55 54 57 58 8 41 42 54 57 17 41 42 54 57 7 43 42 54 55 7 41 42 54 55 8 57 40 41 42 14 40 41 42 54 14 42 54 55 56 12 40 57 58 59 12 # 60 41 42 43 45 6 45 46 49 51 1 46 49 51 52 4 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE GLCA # building block (residue, nucleotide, etc.) # RNME GLCA # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 3 1 2 7 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 12 3 0.40000 0 5 2 3 7 8 10 2 O5 3 16 -0.36000 0 4 3 4 7 13 3 C5 12 3 0.16000 1 5 4 5 10 13 14 4 C6 13 4 0.15000 0 3 5 6 13 5 O6 3 16 -0.54800 0 1 6 6 H6 18 1 0.39800 1 0 7 C2 12 3 0.15000 0 5 8 9 10 11 13 8 O2 3 16 -0.54800 0 2 9 10 9 H2 18 1 0.39800 1 0 10 C3 12 3 0.15000 0 4 11 12 13 14 11 O3 3 16 -0.54800 0 2 12 13 12 H3 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 13 C4 12 3 0.16000 0 14 O4 3 16 -0.36000 0 # bonds # NB 15 # IB JB MCB 1 2 19 1 7 25 2 3 19 3 4 25 3 13 25 4 5 19 5 6 1 7 8 19 7 10 25 8 9 1 # 10 10 11 19 10 13 25 11 12 1 13 14 19 14 15 19 # bond angles # NBA 21 # IB JB KB MCB 0 1 2 8 0 1 7 8 2 1 7 8 1 2 3 9 2 3 4 8 2 3 13 8 4 3 13 7 3 4 5 8 4 5 6 11 1 7 8 8 # 10 1 7 10 7 8 7 10 8 7 8 9 11 7 10 11 8 7 10 13 7 11 10 13 8 10 11 12 11 3 13 10 7 3 13 14 8 10 13 14 8 # 20 13 14 15 9 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 7 0 2 1 2 3 2 4 13 2 7 8 10 1 2 13 7 11 10 2 13 10 14 3 2 # dihedrals # NDA 27 # IB JB KB LB MCB -1 0 1 7 14 0 1 7 10 17 0 1 7 10 7 2 1 7 10 7 2 1 7 8 8 0 1 7 8 8 1 7 8 9 12 1 7 10 13 17 1 7 10 11 7 8 7 10 13 7 # 10 8 7 10 11 8 7 10 11 12 12 7 10 13 3 17 7 10 13 14 7 11 10 13 3 7 11 10 13 14 8 7 1 2 3 14 1 2 3 13 14 13 3 4 5 17 13 3 4 5 7 # 20 2 3 4 5 8 3 4 5 6 12 4 3 13 10 17 2 3 13 10 7 4 3 13 14 7 2 3 13 14 8 10 13 14 15 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE GLCB # building block (residue, nucleotide, etc.) # RNME GLCB # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 12 3 0.40000 0 5 2 3 7 13 14 2 O5 3 16 -0.36000 0 4 3 4 10 13 3 C5 12 3 0.16000 1 5 4 5 7 10 11 4 C6 13 4 0.15000 0 3 5 6 10 5 O6 3 16 -0.54800 0 1 6 6 H6 18 1 0.39800 1 0 7 C3 12 3 0.15000 0 6 8 9 10 11 13 14 8 O3 3 16 -0.54800 0 3 9 10 13 9 H3 18 1 0.39800 1 0 10 C4 12 3 0.15000 0 3 11 12 13 11 O4 3 16 -0.54800 0 1 12 12 H4 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 13 C2 12 3 0.16000 0 14 O2 3 16 -0.36000 0 # bonds # NB 15 # IB JB MCB 1 2 19 1 13 25 2 3 19 3 4 25 3 10 25 4 5 19 5 6 1 7 8 19 7 10 25 7 13 25 # 10 8 9 1 10 11 19 11 12 1 13 14 19 14 15 19 # bond angles # NBA 21 # IB JB KB MCB 0 1 2 8 0 1 13 8 2 1 13 8 1 2 3 9 2 3 4 8 2 3 10 8 4 3 10 7 3 4 5 8 4 5 6 11 8 7 10 8 # 10 10 7 13 7 8 7 13 8 7 8 9 11 3 10 11 8 3 10 7 7 7 10 11 8 10 11 12 11 1 13 7 7 1 13 14 8 7 13 14 8 # 20 13 14 15 9 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 1 0 2 13 2 3 2 4 10 2 7 8 13 10 2 10 7 11 3 2 1 7 14 13 2 # dihedrals # NDA 27 # IB JB KB LB MCB -1 0 1 13 14 0 1 13 7 17 0 1 13 7 7 2 1 13 7 7 2 1 13 14 8 0 1 13 14 8 10 7 13 1 17 8 7 13 1 7 10 7 13 14 7 8 7 13 14 8 # 10 13 7 8 9 12 13 7 10 3 17 13 7 10 11 7 8 7 10 3 7 8 7 10 11 8 7 10 11 12 12 13 1 2 3 14 1 2 3 10 14 10 3 4 5 17 10 3 4 5 7 # 20 2 3 4 5 8 3 4 5 6 12 4 3 10 7 17 2 3 10 7 7 4 3 10 11 7 2 3 10 11 8 1 13 14 15 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE GALB # building block (residue, nucleotide, etc.) # RNME GALB # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 3 1 2 7 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 12 3 0.40000 0 5 2 3 7 8 13 2 O5 3 16 -0.36000 0 4 3 4 7 10 3 C5 12 3 0.16000 1 5 4 5 10 11 13 4 C6 13 4 0.15000 0 3 5 6 10 5 O6 3 16 -0.54800 0 1 6 6 H6 18 1 0.39800 1 0 7 C2 12 3 0.15000 0 5 8 9 10 13 14 8 O2 3 16 -0.54800 0 2 9 13 9 H2 18 1 0.39800 1 0 10 C4 12 3 0.15000 0 4 11 12 13 14 11 O4 3 16 -0.54800 0 2 12 13 12 H4 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 13 C3 12 3 0.16000 0 14 O3 3 16 -0.36000 0 # bonds # NB 15 # IB JB MCB 1 2 19 1 7 25 2 3 19 3 4 25 3 10 25 4 5 19 5 6 1 7 8 19 7 13 25 8 9 1 # 10 10 11 19 10 13 25 11 12 1 13 14 19 14 15 19 # bond angles # NBA 21 # IB JB KB MCB 0 1 2 8 0 1 7 8 2 1 7 8 1 2 3 9 2 3 4 8 2 3 10 8 4 3 10 7 3 4 5 8 4 5 6 11 1 7 8 8 # 10 1 7 13 7 8 7 13 8 7 8 9 11 3 10 11 8 3 10 13 7 11 10 13 8 10 11 12 11 7 13 10 7 7 13 14 8 10 13 14 8 # 20 13 14 15 9 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 1 0 2 7 2 3 2 4 10 2 7 8 13 1 2 10 11 13 3 2 10 7 14 13 2 # dihedrals # NDA 27 # IB JB KB LB MCB -1 0 1 7 14 0 1 7 13 17 0 1 7 13 7 2 1 7 13 7 2 1 7 8 8 0 1 7 8 8 1 7 8 9 12 1 7 13 10 17 1 7 13 14 7 8 7 13 10 7 # 10 8 7 13 14 8 3 10 13 7 17 11 10 13 7 7 3 10 13 14 7 11 10 13 14 8 13 10 11 12 12 7 1 2 3 14 1 2 3 10 14 10 3 4 5 17 10 3 4 5 7 # 20 2 3 4 5 8 3 4 5 6 12 4 3 10 13 17 2 3 10 13 7 4 3 10 11 7 2 3 10 11 8 7 13 14 15 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE # Alan Mark, Urs Stocker 30-4-96 # modified 26-6-96, 5-7-96 # Fe+2 IRON PROTOPROPHYRIN IX # charge -2 ( deprotonated acidic groups) # # Notes: 1) The heme is treated as symmetric # 2) Exclusions are to 1-4 in the rings # #@BLOCKTYPE mtb43b1.dat SOL TYPE HEME # building block (residue, nucleotide, etc.) # RNME HEME # number of atoms, number of preceding exclusions # NMAT NLIN 47 0 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 FE 23 56 0.40000 0 24 2 3 4 5 6 8 9 10 11 18 20 21 22 23 27 29 30 31 32 36 38 39 40 41 2 NA 8 14 -0.10000 0 19 3 4 5 6 7 8 9 10 11 12 13 18 19 20 23 29 32 38 41 3 NB 8 14 -0.10000 0 18 4 5 8 11 18 19 20 21 22 23 24 25 27 28 29 32 38 41 4 NC 8 14 -0.10000 0 17 5 8 11 20 23 27 28 29 30 31 32 33 34 36 37 38 41 5 ND 8 14 -0.10000 1 16 6 7 8 11 20 23 29 32 36 37 38 39 40 41 42 43 6 CHA 11 12 -0.10000 0 11 7 8 9 10 11 13 38 39 40 41 43 7 HHA 17 1 0.10000 1 4 8 9 40 41 8 C1A 11 12 0.00000 0 8 9 10 11 12 13 18 40 41 9 C2A 11 12 0.00000 0 7 10 11 12 13 14 18 41 10 C3A 11 12 0.00000 0 6 11 12 13 18 19 20 11 C4A 11 12 0.00000 1 6 12 13 18 19 20 21 12 CMA 14 5 0.00000 1 2 13 18 13 CAA 13 4 0.00000 0 2 14 15 14 CBA 13 4 0.00000 1 3 15 16 17 15 CGA 11 12 0.72000 0 2 16 17 16 O1A 2 16 -0.36000 0 1 17 17 O2A 2 16 -0.36000 1 0 18 CHB 11 12 -0.10000 0 6 19 20 21 22 23 24 19 HHB 17 1 0.10000 1 2 20 21 20 C1B 11 12 0.00000 0 6 21 22 23 24 25 27 21 C2B 11 12 0.00000 0 5 22 23 24 25 27 22 C3B 11 12 0.00000 0 7 23 24 25 26 27 28 29 23 C4B 11 12 0.00000 1 6 24 25 27 28 29 30 24 CMB 14 5 0.00000 1 1 25 25 CAB 16 3 0.00000 0 2 26 27 26 CBB 13 4 0.00000 1 0 27 CHC 11 12 -0.10000 0 6 28 29 30 31 32 33 28 HHC 17 1 0.10000 1 2 29 30 29 C1C 11 12 0.00000 0 6 30 31 32 33 34 36 30 C2C 11 12 0.00000 0 5 31 32 33 34 36 31 C3C 11 12 0.00000 0 7 32 33 34 35 36 37 38 32 C4C 11 12 0.00000 1 6 33 34 36 37 38 39 33 CMC 14 5 0.00000 1 1 34 34 CAC 16 3 0.00000 0 2 35 36 35 CBC 13 4 0.00000 1 0 36 CHD 11 12 -0.10000 0 6 37 38 39 40 41 42 37 HHD 17 1 0.10000 1 2 38 39 38 C1D 11 12 0.00000 0 5 39 40 41 42 43 39 C2D 11 12 0.00000 0 4 40 41 42 43 40 C3D 11 12 0.00000 0 4 41 42 43 44 41 C4D 11 12 0.00000 1 2 42 43 42 CMD 14 5 0.00000 1 1 43 43 CAD 13 4 0.00000 0 2 44 45 44 CBD 13 4 0.00000 1 3 45 46 47 45 CGD 11 12 0.72000 0 2 46 47 46 O1D 2 16 -0.36000 0 1 47 47 O2D 2 16 -0.36000 1 0 # bonds # NB 54 # IB JB MCB 1 2 34 1 3 34 1 4 34 1 5 34 2 8 13 2 11 13 3 20 13 3 23 13 4 29 13 4 32 13 # 10 5 38 13 5 41 13 6 7 3 6 8 16 6 41 16 8 9 16 9 10 16 9 13 26 10 11 16 10 12 26 # 20 11 18 16 13 14 26 14 15 26 15 16 5 15 17 5 18 19 3 18 20 16 20 21 16 21 22 16 21 24 26 # 30 22 23 16 22 25 26 23 27 16 25 26 11 27 28 3 27 29 16 29 30 16 30 31 16 30 33 26 31 32 16 # 40 31 34 26 32 36 16 34 35 11 36 37 3 36 38 16 38 39 16 39 40 16 39 42 26 40 41 16 40 43 26 # 50 43 44 26 44 45 26 45 46 5 45 47 5 # bond angles # NBA 88 # IB JB KB MCB 2 1 3 1 # 2 1 4 Angle 180 degrees 3 1 4 1 # 2 1 5 Angle 180 degrees 4 1 5 1 2 1 5 1 1 2 8 35 1 2 11 35 8 2 11 5 1 3 20 35 1 3 23 35 20 3 23 5 # 10 1 4 29 35 1 4 32 35 29 4 32 5 1 5 38 35 1 5 41 35 38 5 41 5 7 6 8 19 8 6 41 36 7 6 41 19 2 8 6 32 # 20 2 8 9 14 6 8 9 37 8 9 10 6 8 9 13 36 10 9 13 36 9 10 11 6 9 10 12 36 11 10 12 36 2 11 10 14 2 11 18 32 # 30 10 11 18 37 9 13 14 14 13 14 15 14 14 15 16 21 14 15 17 21 16 15 17 37 11 18 19 19 11 18 20 36 19 18 20 19 3 20 18 32 # 40 3 20 21 14 18 20 21 37 20 21 22 6 20 21 24 36 22 21 24 36 21 22 23 6 21 22 25 36 23 22 25 36 3 23 22 14 3 23 27 32 # 50 22 23 27 37 22 25 26 36 23 27 28 19 23 27 29 36 28 27 29 19 4 29 27 32 4 29 30 14 27 29 30 37 29 30 31 6 29 30 33 36 # 60 31 30 33 36 30 31 32 6 30 31 34 36 32 31 34 36 4 32 31 14 4 32 36 32 31 32 36 37 31 34 35 36 32 36 37 19 32 36 38 36 # 70 37 36 38 19 5 38 36 32 5 38 39 14 36 38 39 37 38 39 40 6 38 39 42 36 40 39 42 36 39 40 41 6 39 40 43 36 41 40 43 36 # 80 5 41 6 32 5 41 40 14 6 41 40 37 40 43 44 14 43 44 45 14 44 45 46 21 44 45 47 21 46 45 47 37 # improper dihedrals # NIDA 46 # IB JB KB LB MCB 1 8 11 2 3 1 20 23 3 3 1 29 32 4 3 1 38 41 5 3 6 2 9 8 1 18 2 10 11 1 18 3 21 20 1 27 3 22 23 1 27 4 30 29 1 36 4 31 32 1 # 10 36 5 39 38 1 6 5 40 41 1 9 8 10 13 1 10 9 11 12 1 21 20 22 24 1 22 21 23 25 1 30 29 31 33 1 31 30 32 34 1 39 38 40 42 1 40 39 41 43 1 # 20 14 16 17 15 1 44 46 47 45 1 7 8 41 6 1 18 11 20 19 1 27 23 29 28 1 36 32 38 37 1 2 8 9 10 1 8 9 10 11 1 9 10 11 2 1 8 2 11 10 1 # 30 11 2 8 9 1 3 20 21 22 1 20 21 22 23 1 21 22 23 3 1 23 3 20 21 1 20 3 23 22 1 4 29 30 31 1 29 30 31 32 1 30 31 32 4 1 32 4 29 30 1 # 40 29 4 32 31 1 5 38 39 40 1 38 39 40 41 1 39 40 41 5 1 41 5 38 39 1 38 5 41 40 1 # dihedrals # NDA 16 # IB JB KB LB MCB 2 11 18 20 5 11 18 20 3 5 3 23 27 29 5 23 27 29 4 5 4 32 36 38 5 32 36 38 5 5 8 6 41 5 5 41 6 8 2 5 8 9 13 14 20 9 13 14 15 17 # 10 13 14 15 16 20 # The torsion barrier for the vinyl still could be too high 21 22 25 26 3 30 31 34 35 3 39 40 43 44 20 40 43 44 45 17 43 44 45 46 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE CYT* # building block (residue, nucleotide, etc.) # RNME CYT* # number of atoms, number of preceding exclusions # NMAT NLIN 35 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C4* 12 3 0.16000 0 7 2 3 14 17 18 22 23 2 O4* 3 16 -0.36000 0 5 3 4 14 17 23 3 C1* 12 3 0.20000 1 9 4 5 6 7 8 13 14 15 17 4 N1 8 14 -0.20000 0 7 5 6 7 8 9 13 14 5 C6 16 3 0.20000 1 6 6 7 8 9 10 13 6 C2 11 12 0.38000 0 5 7 8 9 10 13 7 O2 1 16 -0.38000 1 2 8 9 8 N3 8 14 -0.36000 0 3 9 10 13 9 C4 11 12 0.36000 1 4 10 11 12 13 10 N4 6 14 -0.83000 0 3 11 12 13 11 H41 18 1 0.41500 0 1 12 12 H42 18 1 0.41500 1 0 13 C5 16 3 0.00000 1 0 14 C2* 12 3 0.15000 0 4 15 16 17 18 15 O2* 3 16 -0.54800 0 2 16 17 16 H2* 18 1 0.39800 1 0 17 C3* 12 3 0.00000 1 3 18 19 23 18 O3* 3 16 -0.36000 0 4 19 20 24 27 19 SI1 27 28 0.54000 0 8 20 21 24 25 26 27 28 29 20 OSI 3 16 -0.36000 0 6 21 22 24 27 30 33 21 SI2 27 28 0.54000 0 8 22 23 30 31 32 33 34 35 22 O5* 3 16 -0.36000 1 3 23 30 33 23 C5* 13 4 0.00000 1 0 24 C11 12 3 0.00000 0 3 25 26 27 25 C111 14 5 0.00000 0 1 26 26 C112 14 5 0.00000 1 0 27 C12 12 3 0.00000 0 2 28 29 28 C121 14 5 0.00000 0 1 29 29 C122 14 5 0.00000 1 0 30 C21 12 3 0.00000 0 3 31 32 33 31 C211 14 5 0.00000 0 1 32 32 C212 14 5 0.00000 1 0 33 C22 12 3 0.00000 0 2 34 35 34 C221 14 5 0.00000 0 1 35 35 C222 14 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 37 # IB JB MCB 1 2 19 1 17 25 1 23 25 2 3 19 3 4 22 3 14 25 4 5 16 4 6 16 5 13 15 6 7 4 # 10 6 8 11 8 9 11 9 10 8 9 13 15 10 11 2 10 12 2 14 15 19 14 17 25 15 16 1 17 18 19 # 20 18 19 28 19 20 28 19 24 31 19 27 31 20 21 28 21 22 28 21 30 31 21 33 31 22 23 19 24 25 26 # 30 24 26 26 27 28 26 27 29 26 30 31 26 30 32 26 33 34 26 33 35 26 # bond angles # NBA 57 # IB JB KB MCB 2 1 17 8 2 1 23 8 17 1 23 7 1 2 3 9 2 3 4 8 2 3 14 8 4 3 14 7 3 4 5 26 3 4 6 26 5 4 6 26 # 10 4 5 13 26 4 6 7 26 4 6 8 26 7 6 8 26 6 8 9 26 8 9 10 26 8 9 13 26 10 9 13 26 9 10 11 22 9 10 12 22 # 20 11 10 12 23 5 13 9 26 3 14 15 8 3 14 17 7 15 14 17 8 14 15 16 11 1 17 14 7 1 17 18 8 14 17 18 8 17 18 19 25 # 30 18 19 20 11 18 19 24 11 18 19 27 11 20 19 24 11 20 19 27 11 24 19 27 11 19 20 21 39 20 21 22 11 20 21 30 11 20 21 33 11 # 40 22 21 30 11 22 21 33 11 30 21 33 11 21 22 23 25 1 23 22 8 19 24 25 12 19 24 26 12 25 24 26 14 19 27 28 12 19 27 29 12 # 50 28 27 29 14 21 30 31 12 21 30 32 12 31 30 32 14 21 33 34 12 21 33 35 12 34 33 35 14 # improper dihedrals # NIDA 18 # IB JB KB LB MCB 1 2 23 17 2 17 14 18 1 2 14 15 17 3 2 14 2 4 3 2 4 5 6 3 1 6 4 5 13 1 5 4 6 8 1 4 5 13 9 1 4 6 8 9 1 8 9 13 5 1 # 10 6 8 9 13 1 7 4 8 6 1 10 8 13 9 1 10 11 12 9 1 19 25 26 24 2 19 28 29 27 2 21 31 32 30 2 21 34 35 33 2 # dihedrals # NDA 30 # IB JB KB LB MCB 17 1 23 22 17 17 1 23 22 7 2 1 23 22 8 23 1 17 14 17 23 1 17 18 7 2 1 17 14 7 2 1 17 18 8 3 14 17 1 17 3 14 17 18 7 15 14 17 1 7 # 10 15 14 17 18 8 2 3 14 17 17 2 3 14 17 7 4 3 14 15 7 2 3 14 15 8 17 1 2 3 14 1 2 3 14 14 2 3 4 6 6 8 9 10 11 4 3 14 15 16 12 # 20 1 17 18 19 14 17 18 19 20 14 18 19 20 21 14 19 20 21 22 14 20 21 22 23 14 21 22 23 1 14 18 19 24 25 17 18 19 27 28 17 22 21 30 31 17 22 21 33 34 17 # 30 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE MTXH # building block (residue, nucleotide, etc.) # RNME MTXH # number of atoms, number of preceding exclusions # NMAT NLIN 39 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N1 8 14 -0.28000 0 10 2 3 4 7 8 12 13 15 16 17 2 HA1 18 1 0.28000 0 6 3 4 7 12 16 17 3 C2 11 12 0.00000 1 9 4 5 6 7 8 9 12 16 17 4 NA2 6 14 -0.83000 0 5 5 6 7 8 17 5 HA21 18 1 0.41500 0 1 6 6 HA22 18 1 0.41500 1 0 7 N3 8 14 -0.36000 0 5 8 9 12 13 17 8 C4 11 12 0.36000 1 8 9 10 11 12 13 14 16 17 9 NA4 6 14 -0.83000 0 5 10 11 12 13 17 10 HA41 18 1 0.41500 0 1 11 11 HA42 18 1 0.41500 1 0 12 C4A 11 12 0.00000 0 6 13 14 15 16 17 18 13 N5 8 14 -0.36000 0 5 14 15 16 17 18 14 C6 11 12 0.36000 1 5 15 16 17 18 19 15 C7 16 3 0.36000 0 3 16 17 18 16 N8 8 14 -0.36000 0 2 17 18 17 C8A 11 12 0.00000 1 0 18 C9 13 4 0.00000 0 3 19 20 21 19 N10 10 14 0.00000 0 6 20 21 22 23 24 25 20 CM10 14 5 0.00000 1 1 21 21 C14 11 12 0.00000 0 5 22 23 24 25 26 22 C13 16 3 0.00000 0 5 23 24 25 26 27 23 C15 16 3 0.00000 1 4 24 25 26 27 24 C12 16 3 0.00000 0 3 25 26 27 25 C16 16 3 0.00000 0 2 26 27 26 C11 11 12 0.00000 1 3 27 28 29 27 C 11 12 0.38000 0 4 28 29 30 31 28 O 1 16 -0.38000 1 1 29 29 N 5 14 -0.28000 0 4 30 31 32 37 30 H 18 1 0.28000 1 1 31 31 CA 12 3 0.00000 0 5 32 33 37 38 39 32 CB 13 4 0.00000 0 3 33 34 37 33 CG 13 4 0.00000 1 3 34 35 36 34 CD 11 12 0.72000 0 2 35 36 35 OE1 2 16 -0.36000 0 1 36 36 OE2 2 16 -0.36000 1 0 37 CT 11 12 0.72000 0 2 38 39 38 O1 2 16 -0.36000 0 1 39 39 O2 2 16 -0.36000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 41 # IB JB MCB 1 2 2 1 3 16 1 17 16 3 4 8 3 7 11 4 5 2 4 6 2 7 8 11 8 9 8 8 12 15 # 10 9 10 2 9 11 2 12 13 11 12 17 15 13 14 11 14 15 15 14 18 26 15 16 6 16 17 11 18 19 20 # 20 19 20 20 19 21 10 21 22 15 21 23 15 22 24 15 23 25 15 24 26 15 25 26 15 26 27 26 27 28 4 # 30 27 29 9 29 30 2 29 31 20 31 32 26 31 37 26 32 33 26 33 34 26 34 35 5 34 36 5 37 38 5 # 40 37 39 5 # bond angles # NBA 59 # IB JB KB MCB 2 1 3 24 2 1 17 24 3 1 17 26 1 3 4 26 1 3 7 26 4 3 7 26 3 4 5 22 3 4 6 22 5 4 6 23 3 7 8 26 # 10 7 8 9 26 7 8 12 26 9 8 12 26 8 9 10 22 8 9 11 22 10 9 11 23 8 12 13 26 8 12 17 26 13 12 17 26 12 13 14 26 # 20 13 14 15 26 13 14 18 26 15 14 18 26 14 15 16 26 15 16 17 26 1 17 12 26 1 17 16 26 12 17 16 26 14 18 19 14 18 19 20 19 # 30 18 19 21 32 20 19 21 22 19 21 22 26 19 21 23 26 22 21 23 26 21 22 24 26 21 23 25 26 22 24 26 26 23 25 26 26 24 26 25 26 # 40 24 26 27 26 25 26 27 26 26 27 28 29 26 27 29 18 28 27 29 32 27 29 30 31 27 29 31 30 30 29 31 17 29 31 32 12 29 31 37 12 # 50 32 31 37 12 31 32 33 14 32 33 34 14 33 34 35 21 33 34 36 21 35 34 36 37 31 37 38 21 31 37 39 21 38 37 39 37 # improper dihedrals # NIDA 34 # IB JB KB LB MCB 1 3 17 2 1 3 1 7 4 1 4 5 6 3 1 8 7 12 9 1 9 10 11 8 1 1 3 7 8 1 3 7 8 12 1 7 8 12 17 1 8 12 17 1 1 3 1 17 12 1 # 10 17 1 3 7 1 12 8 13 17 1 17 1 16 12 1 12 13 14 15 1 13 14 15 16 1 14 15 16 17 1 15 16 17 12 1 13 12 17 16 1 17 12 13 14 1 14 13 15 18 1 # 20 19 18 21 20 1 21 22 23 19 1 21 22 24 26 1 21 23 25 26 1 22 21 23 25 1 23 21 22 24 1 22 24 26 25 1 23 25 26 24 1 26 24 25 27 1 27 26 29 28 1 # 30 29 27 31 30 1 31 29 37 32 2 34 35 36 33 1 37 31 39 38 1 # dihedrals # NDA 12 # IB JB KB LB MCB 1 3 4 5 4 12 8 9 10 4 13 14 18 19 20 14 18 19 21 19 18 19 21 22 4 24 26 27 29 1 26 27 29 31 4 27 29 31 37 19 29 31 37 38 20 29 31 32 33 17 # 10 31 32 33 34 17 32 33 34 35 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE FOL # building block (residue, nucleotide, etc.) # RNME FOL # number of atoms, number of preceding exclusions # NMAT NLIN 37 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N1 8 14 -0.36000 0 10 2 3 6 7 8 10 11 13 14 15 2 C2 11 12 0.36000 1 10 3 4 5 6 7 8 9 10 14 15 3 NA2 6 14 -0.83000 0 6 4 5 6 7 8 15 4 HA21 18 1 0.41500 0 1 5 5 HA22 18 1 0.41500 1 0 6 N3 8 14 -0.28000 0 6 7 8 9 10 11 15 7 HA3 18 1 0.28000 1 3 8 9 10 8 C4 11 12 0.38000 0 6 9 10 11 12 14 15 9 OA4 1 16 -0.38000 1 3 10 11 15 10 C4A 11 12 0.00000 0 6 11 12 13 14 15 16 11 N5 8 14 -0.36000 0 5 12 13 14 15 16 12 C6 11 12 0.36000 1 5 13 14 15 16 17 13 C7 16 3 0.36000 0 3 14 15 16 14 N8 8 14 -0.36000 0 2 15 16 15 C8A 11 12 0.00000 1 0 16 C9 13 4 0.00000 0 3 17 18 19 17 N10 10 14 -0.28000 0 6 18 19 20 21 22 23 18 H10 18 1 0.28000 1 1 19 19 C14 11 12 0.00000 0 5 20 21 22 23 24 20 C13 16 3 0.00000 0 5 21 22 23 24 25 21 C15 16 3 0.00000 1 4 22 23 24 25 22 C12 16 3 0.00000 0 3 23 24 25 23 C16 16 3 0.00000 0 2 24 25 24 C11 11 12 0.00000 1 3 25 26 27 25 C 11 12 0.38000 0 4 26 27 28 29 26 O 1 16 -0.38000 1 1 27 27 N 5 14 -0.28000 0 4 28 29 30 35 28 H 18 1 0.28000 1 1 29 29 CA 12 3 0.00000 0 5 30 31 35 36 37 30 CB 13 4 0.00000 0 3 31 32 35 31 CG 13 4 0.00000 1 3 32 33 34 32 CD 11 12 0.72000 0 2 33 34 33 OE1 2 16 -0.36000 0 1 34 34 OE2 2 16 -0.36000 1 0 35 CT 11 12 0.72000 0 2 36 37 36 O1 2 16 -0.36000 0 1 37 37 O2 2 16 -0.36000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 39 # IB JB MCB 1 2 11 1 15 11 2 3 8 2 6 16 3 4 2 3 5 2 6 7 2 6 8 16 8 9 4 8 10 15 # 10 10 11 11 10 15 15 11 12 11 12 13 15 12 16 26 13 14 6 14 15 11 16 17 20 17 18 2 17 19 10 # 20 19 20 15 19 21 15 20 22 15 21 23 15 22 24 15 23 24 15 24 25 26 25 26 4 25 27 9 27 28 2 # 30 27 29 20 29 30 26 29 35 26 30 31 26 31 32 26 32 33 5 32 34 5 35 36 5 35 37 5 # bond angles # NBA 56 # IB JB KB MCB 2 1 15 26 1 2 3 26 1 2 6 26 3 2 6 26 2 3 4 22 2 3 5 22 4 3 5 23 2 6 7 24 2 6 8 26 7 6 8 24 # 10 6 8 9 26 6 8 10 26 9 8 10 26 8 10 11 26 8 10 15 26 11 10 15 26 10 11 12 26 11 12 13 26 11 12 16 26 13 12 16 26 # 20 12 13 14 26 13 14 15 26 1 15 10 26 1 15 14 26 10 15 14 26 12 16 17 14 16 17 18 19 16 17 19 32 18 17 19 22 17 19 20 26 # 30 17 19 21 26 20 19 21 26 19 20 22 26 19 21 23 26 20 22 24 26 21 23 24 26 22 24 23 26 22 24 25 26 23 24 25 26 24 25 26 29 # 40 24 25 27 18 26 25 27 32 25 27 28 31 25 27 29 30 28 27 29 17 27 29 30 12 27 29 35 12 30 29 35 12 29 30 31 14 30 31 32 14 # 50 31 32 33 21 31 32 34 21 33 32 34 37 29 35 36 21 29 35 37 21 36 35 37 37 # improper dihedrals # NIDA 33 # IB JB KB LB MCB 2 1 6 3 1 3 4 5 2 1 6 2 8 7 1 8 6 10 9 1 1 2 6 8 1 2 6 8 10 1 6 8 10 15 1 8 10 15 1 1 2 1 15 10 1 15 1 2 6 1 # 10 10 8 11 15 1 15 1 14 10 1 10 11 12 13 1 11 12 13 14 1 12 13 14 15 1 13 14 15 10 1 11 10 15 14 1 15 10 11 12 1 12 11 13 16 1 17 16 19 18 1 # 20 19 20 21 17 1 19 20 22 24 1 19 21 23 24 1 20 19 21 23 1 21 19 20 22 1 20 22 24 23 1 21 23 24 22 1 24 22 23 25 1 25 24 27 26 1 27 25 29 28 1 # 30 29 27 35 30 2 32 33 34 31 1 35 29 37 36 1 # dihedrals # NDA 11 # IB JB KB LB MCB 1 2 3 4 4 11 12 16 17 20 12 16 17 19 19 16 17 19 20 4 22 24 25 27 1 24 25 27 29 4 25 27 29 35 19 27 29 35 36 20 27 29 30 31 17 29 30 31 32 17 # 10 30 31 32 33 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE DHF # building block (residue, nucleotide, etc.) # RNME DHF # number of atoms, number of preceding exclusions # NMAT NLIN 38 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N1 8 14 -0.36000 0 11 2 3 6 7 8 10 11 13 14 15 16 2 C2 11 12 0.36000 1 10 3 4 5 6 7 8 9 10 14 16 3 NA2 6 14 -0.83000 0 6 4 5 6 7 8 16 4 HA21 18 1 0.41500 0 1 5 5 HA22 18 1 0.41500 1 0 6 N3 8 14 -0.28000 0 6 7 8 9 10 11 16 7 HA3 18 1 0.28000 1 3 8 9 10 8 C4 11 12 0.38000 0 6 9 10 11 12 14 16 9 OA4 1 16 -0.38000 1 3 10 11 16 10 C4A 11 12 0.00000 0 7 11 12 13 14 15 16 17 11 N5 8 14 -0.36000 0 5 12 13 14 16 17 12 C6 11 12 0.36000 1 6 13 14 15 16 17 18 13 C7 13 4 0.00000 0 4 14 15 16 17 14 N8 8 14 -0.28000 0 3 15 16 17 15 HA8 18 1 0.28000 0 1 16 16 C8A 11 12 0.00000 1 0 17 C9 13 4 0.00000 0 3 18 19 20 18 N10 10 14 -0.28000 0 6 19 20 21 22 23 24 19 H10 18 1 0.28000 1 1 20 20 C14 11 12 0.00000 0 5 21 22 23 24 25 21 C13 16 3 0.00000 0 5 22 23 24 25 26 22 C15 16 3 0.00000 1 4 23 24 25 26 23 C12 16 3 0.00000 0 3 24 25 26 24 C16 16 3 0.00000 0 2 25 26 25 C11 11 12 0.00000 1 3 26 27 28 26 C 11 12 0.38000 0 4 27 28 29 30 27 O 1 16 -0.38000 1 1 28 28 N 5 14 -0.28000 0 4 29 30 31 36 29 H 18 1 0.28000 1 1 30 30 CA 12 3 0.00000 0 5 31 32 36 37 38 31 CB 13 4 0.00000 0 3 32 33 36 32 CG 13 4 0.00000 1 3 33 34 35 33 CD 11 12 0.72000 0 2 34 35 34 OE1 2 16 -0.36000 0 1 35 35 OE2 2 16 -0.36000 1 0 36 CT 11 12 0.72000 0 2 37 38 37 O1 2 16 -0.36000 0 1 38 38 O2 2 16 -0.36000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 40 # IB JB MCB 1 2 11 1 16 11 2 3 8 2 6 16 3 4 2 3 5 2 6 7 2 6 8 16 8 9 4 8 10 15 # 10 10 11 11 10 16 15 11 12 11 12 13 14 12 17 26 13 14 16 14 15 2 14 16 16 17 18 20 18 19 2 # 20 18 20 10 20 21 15 20 22 15 21 23 15 22 24 15 23 25 15 24 25 15 25 26 26 26 27 4 26 28 9 # 30 28 29 2 28 30 20 30 31 26 30 36 26 31 32 26 32 33 26 33 34 5 33 35 5 36 37 5 36 38 5 # 40 # bond angles # NBA 58 # IB JB KB MCB 2 1 16 26 1 2 3 26 1 2 6 26 3 2 6 26 2 3 4 22 2 3 5 22 4 3 5 23 2 6 7 24 2 6 8 26 7 6 8 24 # 10 6 8 9 26 6 8 10 26 9 8 10 26 8 10 11 26 8 10 16 26 11 10 16 26 10 11 12 26 11 12 13 26 11 12 17 26 13 12 17 26 # 20 12 13 14 26 13 14 15 24 13 14 16 26 15 14 16 24 1 16 10 26 1 16 14 26 10 16 14 26 12 17 18 14 17 18 19 19 17 18 20 32 # 30 19 18 20 22 18 20 21 26 18 20 22 26 21 20 22 26 20 21 23 26 20 22 24 26 21 23 25 26 22 24 25 26 23 25 24 26 23 25 26 26 # 40 24 25 26 26 25 26 27 29 25 26 28 18 27 26 28 32 26 28 29 31 26 28 30 30 29 28 30 17 28 30 31 12 28 30 36 12 31 30 36 12 # 50 30 31 32 14 31 32 33 14 32 33 34 21 32 33 35 21 34 33 35 37 30 36 37 21 30 36 38 21 37 36 38 37 # improper dihedrals # NIDA 34 # IB JB KB LB MCB 2 1 6 3 1 3 4 5 2 1 6 2 8 7 1 8 6 10 9 1 1 2 6 8 1 2 6 8 10 1 6 8 10 16 1 8 10 16 1 1 2 1 16 10 1 16 1 2 6 1 # 10 10 8 11 16 1 16 1 14 10 1 10 11 12 13 1 11 12 13 14 1 12 13 14 16 1 13 14 16 10 1 11 10 16 14 1 16 10 11 12 1 14 13 16 15 1 12 11 13 17 1 # 20 18 17 20 19 1 20 21 22 18 1 20 21 23 25 1 20 22 24 25 1 21 20 22 24 1 22 20 21 23 1 21 23 25 24 1 22 24 25 23 1 25 23 24 26 1 26 25 28 27 1 # 30 28 26 30 29 1 30 28 36 31 2 33 34 35 32 1 36 30 38 37 1 # dihedrals # NDA 11 # IB JB KB LB MCB 1 2 3 4 4 11 12 17 18 20 12 17 18 20 19 17 18 20 21 4 23 25 26 28 1 25 26 28 30 4 26 28 30 36 19 28 30 36 37 20 28 30 31 32 17 30 31 32 33 17 # 10 31 32 33 34 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE THF # building block (residue, nucleotide, etc.) # RNME THF # number of atoms, number of preceding exclusions # NMAT NLIN 39 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N1 8 14 -0.36000 0 9 2 3 6 7 8 10 11 15 17 2 C2 11 12 0.36000 1 10 3 4 5 6 7 8 9 10 15 17 3 NA2 6 14 -0.83000 0 6 4 5 6 7 8 17 4 HA21 18 1 0.41500 0 1 5 5 HA22 18 1 0.41500 1 0 6 N3 8 14 -0.28000 0 6 7 8 9 10 11 17 7 HA3 18 1 0.28000 1 3 8 9 10 8 C4 11 12 0.38000 0 5 9 10 11 15 17 9 OA4 1 16 -0.38000 1 3 10 11 17 10 C4A 11 12 0.00000 0 5 11 12 13 15 17 11 N5 8 14 -0.28000 0 6 12 13 14 15 17 18 12 HA5 18 1 0.28000 0 1 13 13 C6 12 3 0.00000 1 4 14 15 18 19 14 C7 13 4 0.00000 0 4 15 16 17 18 15 N8 8 14 -0.28000 0 2 16 17 16 HA8 18 1 0.28000 0 1 17 17 C8A 11 12 0.00000 1 0 18 C9 13 4 0.00000 0 3 19 20 21 19 N10 10 14 -0.28000 0 6 20 21 22 23 24 25 20 H10 18 1 0.28000 1 1 21 21 C14 11 12 0.00000 0 5 22 23 24 25 26 22 C13 16 3 0.00000 0 5 23 24 25 26 27 23 C15 16 3 0.00000 1 4 24 25 26 27 24 C12 16 3 0.00000 0 3 25 26 27 25 C16 16 3 0.00000 0 2 26 27 26 C11 11 12 0.00000 1 3 27 28 29 27 C 11 12 0.38000 0 4 28 29 30 31 28 O 1 16 -0.38000 1 1 29 29 N 5 14 -0.28000 0 4 30 31 32 37 30 H 18 1 0.28000 1 1 31 31 CA 12 3 0.00000 0 5 32 33 37 38 39 32 CB 13 4 0.00000 0 3 33 34 37 33 CG 13 4 0.00000 1 3 34 35 36 34 CD 11 12 0.72000 0 2 35 36 35 OE1 2 16 -0.36000 0 1 36 36 OE2 2 16 -0.36000 1 0 37 CT 11 12 0.72000 0 2 38 39 38 O1 2 16 -0.36000 0 1 39 39 O2 2 16 -0.36000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 41 # IB JB MCB 1 2 11 1 17 11 2 3 8 2 6 16 3 4 2 3 5 2 6 7 2 6 8 16 8 9 4 8 10 15 # 10 10 11 16 10 17 15 11 12 2 11 13 22 13 14 25 13 18 26 14 15 22 15 16 2 15 17 16 18 19 20 # 20 19 20 2 19 21 10 21 22 15 21 23 15 22 24 15 23 25 15 24 26 15 25 26 15 26 27 26 27 28 4 # 30 27 29 9 29 30 2 29 31 20 31 32 26 31 37 26 32 33 26 33 34 26 34 35 5 34 36 5 37 38 5 # 40 37 39 5 # bond angles # NBA 60 # IB JB KB MCB 2 1 17 26 1 2 3 26 1 2 6 26 3 2 6 26 2 3 4 22 2 3 5 22 4 3 5 23 2 6 7 24 2 6 8 26 7 6 8 24 # 10 6 8 9 26 6 8 10 26 9 8 10 26 8 10 11 26 8 10 17 26 11 10 17 26 10 11 12 24 10 11 13 26 12 11 13 24 11 13 14 7 # 20 11 13 18 7 14 13 18 7 13 14 15 7 14 15 16 24 14 15 17 26 16 15 17 24 1 17 10 26 1 17 15 26 10 17 15 26 13 18 19 14 # 30 18 19 20 19 18 19 21 32 20 19 21 22 19 21 22 26 19 21 23 26 22 21 23 26 21 22 24 26 21 23 25 26 22 24 26 26 23 25 26 26 # 40 24 26 25 26 24 26 27 26 25 26 27 26 26 27 28 29 26 27 29 18 28 27 29 32 27 29 30 31 27 29 31 30 30 29 31 17 29 31 32 12 # 50 29 31 37 12 32 31 37 12 31 32 33 14 32 33 34 14 33 34 35 21 33 34 36 21 35 34 36 37 31 37 38 21 31 37 39 21 38 37 39 37 # 60 # improper dihedrals # NIDA 35 # IB JB KB LB MCB 2 1 6 3 1 3 4 5 2 1 6 2 8 7 1 8 6 10 9 1 1 2 6 8 1 2 6 8 10 1 6 8 10 17 1 8 10 17 1 1 2 1 17 10 1 17 1 2 6 1 # 10 10 8 11 17 1 17 1 15 10 1 10 11 13 14 1 11 13 14 15 1 13 14 15 17 1 14 15 17 10 1 11 10 17 15 1 17 10 11 13 1 11 10 13 12 1 15 14 17 16 1 # 20 13 11 14 18 1 19 18 21 20 1 21 22 23 19 1 21 22 24 26 1 21 23 25 26 1 22 21 23 25 1 23 21 22 24 1 22 24 26 25 1 23 25 26 24 1 26 24 25 27 1 # 30 27 26 29 28 1 29 27 31 30 1 31 29 37 32 2 34 35 36 33 1 37 31 39 38 1 # dihedrals # NDA 11 # IB JB KB LB MCB 1 2 3 4 4 11 13 18 19 20 13 18 19 21 19 18 19 21 22 4 24 26 27 29 1 26 27 29 31 4 27 29 31 37 19 29 31 37 38 20 29 31 32 33 17 31 32 33 34 17 # 10 32 33 34 35 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE TMP # building block (residue, nucleotide, etc.) # RNME TMP # number of atoms, number of preceding exclusions # NMAT NLIN 25 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N1 8 14 -0.36000 0 7 2 3 6 7 11 12 13 2 C2 11 12 0.36000 1 8 3 4 5 6 7 8 11 12 3 NA2 6 14 -0.83000 0 5 4 5 6 7 12 4 HA21 18 1 0.41500 0 1 5 5 HA22 18 1 0.41500 1 0 6 N3 8 14 -0.36000 0 5 7 8 11 12 13 7 C4 11 12 0.36000 1 6 8 9 10 11 12 13 8 NA4 6 14 -0.83000 0 5 9 10 11 12 13 9 HA41 18 1 0.41500 0 1 10 10 HA42 18 1 0.41500 1 0 11 C5 11 12 0.00000 0 3 12 13 14 12 C6 16 3 0.00000 0 1 13 13 C7 13 4 0.00000 1 5 14 15 16 17 20 14 C11 11 12 0.00000 0 7 15 16 17 18 20 21 23 15 C12 16 3 0.00000 0 6 16 17 18 20 23 24 16 C16 16 3 0.00000 1 5 17 20 21 23 24 17 C13 11 12 0.18000 0 6 18 19 20 21 23 24 18 O13 3 16 -0.36000 0 4 19 20 23 24 19 CM13 14 5 0.18000 1 0 20 C15 11 12 0.18000 0 4 21 22 23 24 21 O15 3 16 -0.36000 0 3 22 23 24 22 CM15 14 5 0.18000 1 0 23 C14 11 12 0.18000 0 2 24 25 24 O14 3 16 -0.36000 0 1 25 25 CM14 14 5 0.18000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 26 # IB JB MCB 1 2 11 1 12 6 2 3 8 2 6 11 3 4 2 3 5 2 6 7 11 7 8 8 7 11 15 8 9 2 # 10 8 10 2 11 12 15 11 13 26 13 14 26 14 15 15 14 16 15 15 17 15 16 20 15 17 18 12 17 23 15 # 20 18 19 17 20 21 12 20 23 15 21 22 17 23 24 12 24 25 17 # bond angles # NBA 36 # IB JB KB MCB 2 1 12 26 1 2 3 26 1 2 6 26 3 2 6 26 2 3 4 22 2 3 5 22 4 3 5 23 2 6 7 26 6 7 8 26 6 7 11 26 # 10 8 7 11 26 7 8 9 22 7 8 10 22 9 8 10 23 7 11 12 26 7 11 13 26 12 11 13 26 1 12 11 26 11 13 14 14 13 14 15 26 # 20 13 14 16 26 15 14 16 26 14 15 17 26 14 16 20 26 15 17 18 26 15 17 23 26 18 17 23 26 17 18 19 19 16 20 21 26 16 20 23 26 # 30 21 20 23 26 20 21 22 19 17 23 20 26 17 23 24 26 20 23 24 26 23 24 25 19 # improper dihedrals # NIDA 21 # IB JB KB LB MCB 2 1 6 3 1 3 4 5 2 1 7 6 11 8 1 8 9 10 7 1 1 2 6 7 1 2 6 7 11 1 6 7 11 12 1 7 11 12 1 1 2 1 12 11 1 12 1 2 6 1 # 10 11 7 12 13 1 14 15 16 13 1 14 15 17 23 1 14 16 20 23 1 15 17 23 20 1 15 14 16 20 1 16 20 23 17 1 16 14 15 17 1 17 15 18 23 1 20 16 21 23 1 # 20 23 17 24 20 1 # dihedrals # NDA 9 # IB JB KB LB MCB 1 2 3 4 4 11 7 8 9 4 7 11 13 14 20 11 13 14 15 20 15 17 18 19 2 15 17 18 19 3 16 20 21 22 2 16 20 21 22 3 17 23 24 25 2 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE TMPH # building block (residue, nucleotide, etc.) # RNME TMPH # number of atoms, number of preceding exclusions # NMAT NLIN 26 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N1 8 14 -0.28000 0 8 2 3 4 7 8 12 13 14 2 HA1 18 1 0.28000 0 5 3 4 7 12 13 3 C2 11 12 0.00000 1 8 4 5 6 7 8 9 12 13 4 NA2 6 14 -0.83000 0 5 5 6 7 8 13 5 HA21 18 1 0.41500 0 1 6 6 HA22 18 1 0.41500 1 0 7 N3 8 14 -0.36000 0 5 8 9 12 13 14 8 C4 11 12 0.36000 1 6 9 10 11 12 13 14 9 NA4 6 14 -0.83000 0 5 10 11 12 13 14 10 HA41 18 1 0.41500 0 1 11 11 HA42 18 1 0.41500 1 0 12 C5 11 12 0.00000 0 3 13 14 15 13 C6 16 3 0.00000 0 1 14 14 C7 13 4 0.00000 1 5 15 16 17 18 21 15 C11 11 12 0.00000 0 7 16 17 18 19 21 22 24 16 C12 16 3 0.00000 0 6 17 18 19 21 24 25 17 C16 16 3 0.00000 1 5 18 21 22 24 25 18 C13 11 12 0.18000 0 6 19 20 21 22 24 25 19 O13 3 16 -0.36000 0 4 20 21 24 25 20 CM13 14 5 0.18000 1 0 21 C15 11 12 0.18000 0 4 22 23 24 25 22 O15 3 16 -0.36000 0 3 23 24 25 23 CM15 14 5 0.18000 1 0 24 C14 11 12 0.18000 0 2 25 26 25 O14 3 16 -0.36000 0 1 26 26 CM14 14 5 0.18000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 27 # IB JB MCB 1 2 2 1 3 16 1 13 16 3 4 8 3 7 11 4 5 2 4 6 2 7 8 11 8 9 8 8 12 15 # 10 9 10 2 9 11 2 12 13 15 12 14 26 14 15 26 15 16 15 15 17 15 16 18 15 17 21 15 18 19 12 # 20 18 24 15 19 20 17 21 22 12 21 24 15 22 23 17 24 25 12 25 26 17 # bond angles # NBA 38 # IB JB KB MCB 2 1 3 24 2 1 13 24 3 1 13 26 1 3 4 26 1 3 7 26 4 3 7 26 3 4 5 22 3 4 6 22 5 4 6 23 3 7 8 26 # 10 7 8 9 26 7 8 12 26 9 8 12 26 8 9 10 22 8 9 11 22 10 9 11 23 8 12 13 26 8 12 14 26 13 12 14 26 1 13 12 26 # 20 12 14 15 14 14 15 16 26 14 15 17 26 16 15 17 26 15 16 18 26 15 17 21 26 16 18 19 26 16 18 24 26 19 18 24 26 18 19 20 19 # 30 17 21 22 26 17 21 24 26 22 21 24 26 21 22 23 19 18 24 21 26 18 24 25 26 21 24 25 26 24 25 26 19 # improper dihedrals # NIDA 22 # IB JB KB LB MCB 1 3 13 2 1 3 1 7 4 1 4 5 6 3 1 8 7 12 9 1 9 10 11 8 1 1 3 7 8 1 3 7 8 12 1 7 8 12 13 1 8 12 13 1 1 3 1 13 12 1 # 10 13 1 3 7 1 12 8 13 14 1 15 16 17 14 1 15 16 18 24 1 15 17 21 24 1 16 18 24 21 1 16 15 17 21 1 17 21 24 18 1 17 15 16 18 1 18 16 19 24 1 # 20 21 17 22 24 1 24 18 25 21 1 # dihedrals # NDA 9 # IB JB KB LB MCB 1 3 4 5 4 12 8 9 10 4 8 12 14 15 20 12 14 15 16 20 16 18 19 20 2 16 18 19 20 3 17 21 22 23 2 17 21 22 23 3 18 24 25 26 2 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE TMPHP # building block (residue, nucleotide, etc.) # RNME TMPHP # number of atoms, number of preceding exclusions # NMAT NLIN 26 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N1 8 14 -0.36000 0 8 2 3 4 7 8 12 13 14 2 HA1 18 1 0.36000 0 5 3 4 7 12 13 3 C2 11 12 0.00000 1 8 4 5 6 7 8 9 12 13 4 NA2 6 14 -0.83000 0 5 5 6 7 8 13 5 HA21 18 1 0.41500 0 1 6 6 HA22 18 1 0.41500 1 0 7 N3 8 14 -0.36000 0 5 8 9 12 13 14 8 C4 11 12 0.36000 1 6 9 10 11 12 13 14 9 NA4 6 14 -0.83000 0 5 10 11 12 13 14 10 HA41 18 1 0.41500 0 1 11 11 HA42 18 1 0.41500 1 0 12 C5 11 12 0.00000 0 3 13 14 15 13 C6 16 3 0.00000 0 1 14 14 C7 13 4 0.00000 1 5 15 16 17 18 21 15 C11 11 12 0.00000 0 7 16 17 18 19 21 22 24 16 C12 16 3 0.00000 0 6 17 18 19 21 24 25 17 C16 16 3 0.00000 1 5 18 21 22 24 25 18 C13 11 12 0.18000 0 6 19 20 21 22 24 25 19 O13 3 16 -0.36000 0 4 20 21 24 25 20 CM13 14 5 0.18000 1 0 21 C15 11 12 0.18000 0 4 22 23 24 25 22 O15 3 16 -0.36000 0 3 23 24 25 23 CM15 14 5 0.18000 1 0 24 C14 11 12 0.18000 0 2 25 26 25 O14 3 16 -0.36000 0 1 26 26 CM14 14 5 0.18000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 27 # IB JB MCB 1 2 2 1 3 16 1 13 16 3 4 8 3 7 11 4 5 2 4 6 2 7 8 11 8 9 8 8 12 15 # 10 9 10 2 9 11 2 12 13 15 12 14 26 14 15 26 15 16 15 15 17 15 16 18 15 17 21 15 18 19 12 # 20 18 24 15 19 20 17 21 22 12 21 24 15 22 23 17 24 25 12 25 26 17 # bond angles # NBA 38 # IB JB KB MCB 2 1 3 24 2 1 13 24 3 1 13 26 1 3 4 26 1 3 7 26 4 3 7 26 3 4 5 22 3 4 6 22 5 4 6 23 3 7 8 26 # 10 7 8 9 26 7 8 12 26 9 8 12 26 8 9 10 22 8 9 11 22 10 9 11 23 8 12 13 26 8 12 14 26 13 12 14 26 1 13 12 26 # 20 12 14 15 14 14 15 16 26 14 15 17 26 16 15 17 26 15 16 18 26 15 17 21 26 16 18 19 26 16 18 24 26 19 18 24 26 18 19 20 19 # 30 17 21 22 26 17 21 24 26 22 21 24 26 21 22 23 19 18 24 21 26 18 24 25 26 21 24 25 26 24 25 26 19 # improper dihedrals # NIDA 22 # IB JB KB LB MCB 1 3 13 2 1 3 1 7 4 1 4 5 6 3 1 8 7 12 9 1 9 10 11 8 1 1 3 7 8 1 3 7 8 12 1 7 8 12 13 1 8 12 13 1 1 3 1 13 12 1 # 10 13 1 3 7 1 12 8 13 14 1 15 16 17 14 1 15 16 18 24 1 15 17 21 24 1 16 18 24 21 1 16 15 17 21 1 17 21 24 18 1 17 15 16 18 1 18 16 19 24 1 # 20 21 17 22 24 1 24 18 25 21 1 # dihedrals # NDA 9 # IB JB KB LB MCB 1 3 4 5 4 12 8 9 10 4 8 12 14 15 20 12 14 15 16 20 16 18 19 20 2 16 18 19 20 3 17 21 22 23 2 17 21 22 23 3 18 24 25 26 2 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE PDG # building block (residue, nucleotide, etc.) # RNME PDG # number of atoms, number of preceding exclusions # NMAT NLIN 13 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 27 31 1.08000 0 6 2 3 4 5 6 7 2 O1P 2 16 -0.36000 0 4 3 4 5 6 3 O2P 2 16 -0.36000 0 3 4 5 6 4 O3P 3 16 -0.54800 0 2 5 6 5 H3P 18 1 0.39800 0 1 6 6 O4P 3 16 -0.36000 0 2 7 8 7 C1 13 4 0.15000 1 3 8 9 11 8 C2 12 3 0.15000 0 5 9 10 11 12 13 9 O2 3 16 -0.54800 0 2 10 11 10 H2 18 1 0.39800 1 0 11 C3 11 12 0.72000 0 2 12 13 12 OT1 2 16 -0.36000 0 1 13 13 OT2 2 16 -0.36000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 12 # IB JB MCB 1 2 23 1 3 23 1 4 27 1 6 27 4 5 1 6 7 17 7 8 26 8 9 17 8 11 26 9 10 1 # 10 11 12 5 11 13 5 # bond angles # NBA 16 # IB JB KB MCB 2 1 3 28 2 1 4 13 2 1 6 13 3 1 4 13 3 1 6 13 4 1 6 4 1 4 5 11 1 6 7 25 6 7 8 14 7 8 9 14 # 10 7 8 11 12 9 8 11 12 8 9 10 11 8 11 12 21 8 11 13 21 12 11 13 37 # improper dihedrals # NIDA 2 # IB JB KB LB MCB 8 7 11 9 2 11 8 13 12 1 # dihedrals # NDA 8 # IB JB KB LB MCB 6 1 4 5 11 6 1 4 5 9 4 1 6 7 11 4 1 6 7 9 1 6 7 8 14 6 7 8 11 17 7 8 9 10 12 7 8 11 12 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE ATP # building block (residue, nucleotide, etc.) # RNME ATP # number of atoms, number of preceding exclusions # NMAT NLIN 36 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 AN9 8 14 -0.20000 0 10 2 3 4 6 10 11 12 13 14 16 2 AC4 11 12 0.20000 1 9 3 4 5 6 7 10 11 12 13 3 AN3 8 14 -0.36000 0 7 4 5 6 10 11 12 13 4 AC2 16 3 0.36000 1 4 5 6 7 10 5 AN1 8 14 -0.36000 0 4 6 7 10 11 6 AC6 11 12 0.36000 1 6 7 8 9 10 11 12 7 AN6 6 14 -0.83000 0 4 8 9 10 11 8 AH61 18 1 0.41500 0 1 9 9 AH62 18 1 0.41500 1 0 10 AC5 11 12 0.00000 0 3 11 12 13 11 AN7 8 14 -0.36000 0 2 12 13 12 AC8 16 3 0.36000 1 1 13 13 AC1* 12 3 0.20000 0 5 14 15 16 17 19 14 AO4* 3 16 -0.36000 0 4 15 16 19 22 15 AC4* 12 3 0.16000 1 5 16 19 20 22 23 16 AC2* 12 3 0.15000 0 4 17 18 19 20 17 AO2* 3 16 -0.54800 0 2 18 19 18 AH2* 18 1 0.39800 1 0 19 AC3* 12 3 0.15000 0 3 20 21 22 20 AO3* 3 16 -0.54800 0 1 21 21 AH3* 18 1 0.39800 1 0 22 AC5* 13 4 0.00000 1 2 23 24 23 AO5* 3 16 -0.36000 0 4 24 25 26 27 24 APA 27 31 1.15500 0 4 25 26 27 28 25 AO1PA 2 16 -0.36000 0 2 26 27 26 AO2PA 2 16 -0.36000 1 1 27 27 AO3PA 3 16 -0.36000 0 4 28 29 30 31 28 APB 27 31 1.15500 0 4 29 30 31 32 29 AO1PB 2 16 -0.36000 0 2 30 31 30 AO2PB 2 16 -0.36000 1 1 31 31 AO3PB 3 16 -0.36000 0 5 32 33 34 35 36 32 APG 27 31 1.08000 0 4 33 34 35 36 33 AO1PG 2 16 -0.36000 0 3 34 35 36 34 AO2PG 2 16 -0.36000 0 2 35 36 35 AO3PG 3 16 -0.54800 0 1 36 36 AH3PG 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 38 # IB JB MCB 1 2 9 1 12 9 1 13 21 2 3 11 2 10 15 3 4 6 4 5 6 5 6 11 6 7 8 6 10 15 # 10 7 8 2 7 9 2 10 11 9 11 12 9 13 14 19 13 16 25 14 15 19 15 19 25 15 22 25 16 17 19 # 20 16 19 25 17 18 1 19 20 19 20 21 1 22 23 19 23 24 27 24 25 23 24 26 23 24 27 27 27 28 27 # 30 28 29 23 28 30 23 28 31 27 31 32 27 32 33 23 32 34 23 32 35 27 35 36 1 # bond angles # NBA 58 # IB JB KB MCB 2 1 12 6 2 1 13 36 12 1 13 36 1 2 3 38 1 2 10 6 3 2 10 26 2 3 4 26 3 4 5 26 4 5 6 26 5 6 7 26 # 10 5 6 10 26 7 6 10 26 6 7 8 22 6 7 9 22 8 7 9 23 2 10 6 26 2 10 11 6 6 10 11 38 10 11 12 6 1 12 11 6 # 20 1 13 14 8 1 13 16 8 14 13 16 8 13 14 15 9 14 15 19 8 14 15 22 8 19 15 22 7 13 16 17 8 13 16 19 7 17 16 19 8 # 30 16 17 18 11 15 19 16 7 15 19 20 8 16 19 20 8 19 20 21 11 15 22 23 8 22 23 24 25 23 24 25 13 23 24 26 13 23 24 27 4 # 40 25 24 26 28 25 24 27 13 26 24 27 13 24 27 28 25 27 28 29 13 27 28 30 13 27 28 31 4 29 28 30 28 29 28 31 13 30 28 31 13 # 50 28 31 32 25 31 32 33 13 31 32 34 13 31 32 35 4 33 32 34 28 33 32 35 13 34 32 35 13 32 35 36 11 # improper dihedrals # NIDA 20 # IB JB KB LB MCB 13 2 12 1 1 2 1 12 11 1 12 1 2 10 1 10 11 12 1 1 1 2 10 11 1 2 10 11 12 1 2 1 3 10 1 10 6 11 2 1 3 2 10 6 1 5 6 10 2 1 # 10 10 2 3 4 1 4 5 6 10 1 2 3 4 5 1 3 4 5 6 1 7 5 10 6 1 7 8 9 6 1 13 1 14 16 2 15 14 22 19 2 16 17 19 13 2 19 16 20 15 2 # 20 # dihedrals # NDA 34 # IB JB KB LB MCB 10 6 7 8 4 2 1 13 14 6 13 16 17 18 12 15 19 20 21 12 16 13 14 15 14 13 14 15 19 14 14 13 16 19 17 14 13 16 19 7 1 13 16 17 7 14 13 16 17 8 # 10 13 16 19 15 17 13 16 19 20 7 17 16 19 15 7 17 16 19 20 8 22 15 19 16 17 22 15 19 20 7 14 15 19 16 7 14 15 19 20 8 19 15 22 23 17 19 15 22 23 7 # 20 14 15 22 23 8 15 22 23 24 14 22 23 24 27 11 22 23 24 27 9 23 24 27 28 11 23 24 27 28 9 24 27 28 31 11 24 27 28 31 9 27 28 31 32 11 27 28 31 32 9 # 30 28 31 32 35 11 28 31 32 35 9 31 32 35 36 11 31 32 35 36 9 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE PMB # building block (residue, nucleotide, etc.) # RNME PMB # number of atoms, number of preceding exclusions # NMAT NLIN 11 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 PC8 14 5 0.00000 0 5 2 3 4 5 6 2 PC5 11 12 0.00000 0 5 3 4 5 6 7 3 PC4 16 3 0.00000 0 5 4 5 6 7 8 4 PC6 16 3 0.00000 1 4 5 6 7 8 5 PC3 16 3 0.00000 0 3 6 7 8 6 PC7 16 3 0.00000 0 2 7 8 7 PC2 11 12 0.00000 1 4 8 9 10 11 8 PC1 11 12 0.50000 0 3 9 10 11 9 PO 2 16 -0.30000 0 2 10 11 10 PHC1 17 1 -0.10000 0 1 11 11 PHC2 17 1 -0.10000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 11 # IB JB MCB 1 2 26 2 3 15 2 4 15 3 5 15 4 6 15 5 7 15 6 7 15 7 8 26 8 9 18 8 10 3 # 10 8 11 3 # bond angles # NBA 16 # IB JB KB MCB 1 2 3 26 1 2 4 26 3 2 4 26 2 3 5 26 2 4 6 26 3 5 7 26 4 6 7 26 5 7 6 26 5 7 8 26 6 7 8 26 # 10 7 8 9 12 7 8 10 10 7 8 11 10 9 8 10 10 9 8 11 10 10 8 11 9 # improper dihedrals # NIDA 8 # IB JB KB LB MCB 2 3 4 1 1 4 2 3 5 1 3 2 4 6 1 2 3 5 7 1 2 4 6 7 1 3 5 7 6 1 4 6 7 5 1 7 5 6 8 1 # dihedrals # NDA 1 # IB JB KB LB MCB 5 7 8 9 20 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE PMBH # building block (residue, nucleotide, etc.) # RNME PMBH # number of atoms, number of preceding exclusions # NMAT NLIN 12 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 PC8 14 5 0.00000 0 5 2 3 4 5 6 2 PC5 11 12 0.00000 0 5 3 4 5 6 7 3 PC4 16 3 0.00000 0 5 4 5 6 7 8 4 PC6 16 3 0.00000 1 4 5 6 7 8 5 PC3 16 3 0.00000 0 3 6 7 8 6 PC7 16 3 0.00000 0 2 7 8 7 PC2 11 12 0.00000 1 4 8 9 11 12 8 PC1 11 12 -0.05000 0 4 9 10 11 12 9 PO 3 16 -0.54800 0 3 10 11 12 10 PH 18 1 0.39800 0 0 11 PHC1 17 1 0.10000 0 1 12 12 PHC2 17 1 0.10000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 12 # IB JB MCB 1 2 26 2 3 15 2 4 15 3 5 15 4 6 15 5 7 15 6 7 15 7 8 26 8 9 12 9 10 1 # 10 8 11 3 8 12 3 # bond angles # NBA 17 # IB JB KB MCB 1 2 3 26 1 2 4 26 3 2 4 26 2 3 5 26 2 4 6 26 3 5 7 26 4 6 7 26 5 7 6 26 5 7 8 26 6 7 8 26 # 10 7 8 9 12 8 9 10 11 7 8 11 10 7 8 12 10 9 8 11 10 9 8 12 10 11 8 12 9 # improper dihedrals # NIDA 8 # IB JB KB LB MCB 2 3 4 1 1 4 2 3 5 1 3 2 4 6 1 2 3 5 7 1 2 4 6 7 1 3 5 7 6 1 4 6 7 5 1 7 5 6 8 1 # dihedrals # NDA 2 # IB JB KB LB MCB 5 7 8 9 20 7 8 9 10 12 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE BA # building block (residue, nucleotide, etc.) # RNME BA # number of atoms, number of preceding exclusions # NMAT NLIN 15 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C3 11 12 -0.10000 0 10 2 3 4 5 6 7 8 9 10 11 2 H3 17 1 0.10000 1 6 3 4 5 6 7 9 3 C2 11 12 -0.10000 0 8 4 5 6 7 8 9 11 12 4 H2 17 1 0.10000 1 4 5 7 8 11 5 C4 11 12 -0.10000 0 6 6 7 9 10 11 12 6 H4 17 1 0.10000 1 3 9 10 11 7 C1 11 12 -0.10000 0 5 8 9 10 11 12 8 H1 17 1 0.10000 1 3 9 11 12 9 C5 11 12 -0.10000 0 3 10 11 12 10 H5 17 1 0.10000 1 2 11 12 11 C6 11 12 0.00000 1 3 12 13 14 12 C7 11 12 0.53000 0 3 13 14 15 13 O8 1 16 -0.38000 0 1 14 14 O9 3 16 -0.54800 0 1 15 15 H9 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 15 # IB JB MCB 1 2 3 1 3 15 1 5 15 3 4 3 3 7 15 5 6 3 5 9 15 7 8 3 7 11 15 9 10 3 # 10 9 11 15 11 12 22 12 13 4 12 14 12 14 15 1 # bond angles # NBA 22 # IB JB KB MCB 2 1 3 24 2 1 5 24 3 1 5 26 1 3 4 24 1 3 7 26 4 3 7 24 1 5 6 24 1 5 9 26 6 5 9 24 3 7 8 24 # 10 3 7 11 26 8 7 11 24 5 9 10 24 5 9 11 26 10 9 11 24 7 11 9 26 7 11 12 26 9 11 12 26 11 12 13 29 11 12 14 18 # 20 13 12 14 32 12 14 15 11 # improper dihedrals # NIDA 13 # IB JB KB LB MCB 1 3 5 2 1 4 1 7 3 1 6 1 9 5 1 7 3 11 8 1 9 5 11 10 1 1 3 7 11 1 1 5 9 11 1 3 1 5 9 1 5 1 3 7 1 3 7 11 9 1 # 10 5 9 11 7 1 11 7 9 12 1 12 13 14 11 1 # dihedrals # NDA 2 # IB JB KB LB MCB 7 11 12 14 1 11 12 14 15 3 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE RTOL # building block (residue, nucleotide, etc.) # RNME RTOL # number of atoms, number of preceding exclusions # NMAT NLIN 22 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C18 14 5 0.00000 0 4 2 3 4 9 2 C17 14 5 0.00000 0 3 3 4 9 3 C1 11 12 0.00000 1 5 4 5 7 9 10 4 C2 13 4 0.00000 0 3 5 6 9 5 C3 13 4 0.00000 0 2 6 7 6 C4 13 4 0.00000 1 3 7 8 9 7 C5 11 12 0.00000 0 3 8 9 10 8 C16 14 5 0.00000 0 1 9 9 C6 11 12 0.00000 1 2 10 11 10 C7 16 3 0.00000 0 2 11 12 11 C8 16 3 0.00000 1 3 12 13 14 12 C9 11 12 0.00000 0 3 13 14 15 13 C19 14 5 0.00000 0 1 14 14 C10 16 3 0.00000 1 2 15 16 15 C11 16 3 0.00000 0 2 16 17 16 C12 16 3 0.00000 1 3 17 18 19 17 C13 11 12 0.00000 0 3 18 19 20 18 C20 14 5 0.00000 0 1 19 19 C14 16 3 0.00000 1 2 20 21 20 C15 13 4 0.15000 0 2 21 22 21 O21 3 16 -0.54800 0 1 22 22 H21 18 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 22 # IB JB MCB 1 3 26 2 3 26 3 4 26 3 9 26 4 5 26 5 6 26 6 7 26 7 8 26 7 9 9 9 10 22 # 10 10 11 12 11 12 22 12 13 26 12 14 12 14 15 22 15 16 12 16 17 22 17 18 26 17 19 12 19 20 22 # 20 20 21 17 21 22 1 # bond angles # NBA 29 # IB JB KB MCB 1 3 2 12 1 3 4 12 1 3 9 12 2 3 4 12 2 3 9 12 4 3 9 12 3 4 5 12 4 5 6 12 5 6 7 12 6 7 8 26 # 10 6 7 9 26 8 7 9 26 3 9 7 26 3 9 10 26 7 9 10 26 9 10 11 26 10 11 12 26 11 12 13 26 11 12 14 26 13 12 14 26 # 20 12 14 15 26 14 15 16 26 15 16 17 26 16 17 18 26 16 17 19 26 18 17 19 26 17 19 20 26 19 20 21 12 20 21 22 11 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 7 6 9 8 1 9 3 10 7 1 12 11 14 13 1 17 16 19 18 1 # dihedrals # NDA 16 # IB JB KB LB MCB 3 4 5 6 17 9 3 4 5 17 4 5 6 7 17 4 3 9 7 17 5 6 7 9 17 6 7 9 3 4 7 9 10 11 17 9 10 11 12 4 10 11 12 14 3 11 12 14 15 4 # 10 12 14 15 16 3 14 15 16 17 4 15 16 17 19 3 16 17 19 20 4 17 19 20 21 20 19 20 21 22 12 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE TEMP # building block (residue, nucleotide, etc.) # RNME TEMP # number of atoms, number of preceding exclusions # NMAT NLIN 12 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 O1 1 16 -0.20000 0 9 2 3 4 5 6 7 8 9 10 2 N1 8 14 -0.03600 0 9 3 4 5 6 7 8 9 10 11 3 C1 11 12 0.11800 0 8 4 5 6 7 8 9 10 11 4 C4 11 12 0.11800 1 7 5 6 7 8 9 10 11 5 CA 11 12 0.00000 0 8 6 7 8 9 10 11 12 13 6 C3 16 3 0.00000 1 5 7 8 9 10 11 7 C6 14 5 0.00000 1 2 8 11 8 C7 14 5 0.00000 1 1 11 9 C8 14 5 0.00000 1 1 10 10 C9 14 5 0.00000 1 0 11 C5 11 12 0.38000 0 0 12 O5 1 16 -0.38000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 13 # IB JB MCB 1 2 5 2 3 21 2 4 21 3 5 24 3 7 25 3 8 25 4 6 24 4 9 25 4 10 25 5 6 6 # 10 5 11 22 11 12 4 11 13 9 # bond angles # NBA 22 # IB JB KB MCB 1 2 3 30 1 2 4 30 3 2 4 18 2 3 5 2 2 3 7 12 2 3 8 12 5 3 7 15 5 3 8 15 7 3 8 14 3 5 6 15 # 10 3 5 11 30 6 5 11 34 4 6 5 15 2 4 6 2 2 4 9 12 2 4 10 12 6 4 9 15 6 4 10 15 9 4 10 14 5 11 12 29 # 20 5 11 13 18 12 11 13 32 # improper dihedrals # NIDA 8 # IB JB KB LB MCB 2 3 4 1 1 2 3 5 6 1 3 5 6 4 1 2 4 6 5 1 3 2 4 6 1 4 2 3 5 1 5 3 6 11 1 11 5 13 12 1 # dihedrals # NDA 1 # IB JB KB LB MCB 6 5 11 13 4 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE ETH # building block (residue, nucleotide, etc.) # RNME ETH # 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 EO 2 16 -0.36000 0 2 2 3 2 EC1 13 4 0.36000 0 1 3 3 EC2 14 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 2 # IB JB MCB 1 2 18 2 3 26 # bond angles # NBA 1 # IB JB KB MCB 1 2 3 12 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE ETHH # building block (residue, nucleotide, etc.) # RNME ETHH # 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 EH 18 1 0.39800 0 2 2 3 2 EO 3 16 -0.54800 0 2 3 4 3 EC1 13 4 0.15000 1 1 4 4 EC2 14 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 3 # IB JB MCB 1 2 1 2 3 17 3 4 26 # bond angles # NBA 2 # IB JB KB MCB 1 2 3 11 2 3 4 14 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 1 2 3 4 12 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb43b1.dat SOL TYPE CH4 # building block (residue, nucleotide, etc.) # RNME CH4 # number of atoms, number of preceding exclusions # NMAT NLIN 1 0 # atoms #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 CM 15 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 mtb43b1.dat SOL TYPE AR # building block (residue, nucleotide, etc.) # RNME AR # number of atoms, number of preceding exclusions # NMAT NLIN 1 0 # atoms #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 AR 28 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 mtb43b1.dat SOL TYPE SO42- # 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 20 32 1.44000 0 4 2 3 4 5 2 IO1 2 16 -0.36000 0 3 3 4 5 3 IO2 2 16 -0.36000 0 2 4 5 4 IO3 2 16 -0.36000 0 1 5 5 IO4 2 16 -0.36000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 4 # IB JB MCB 1 2 24 1 3 24 1 4 24 1 5 24 # bond angles # NBA 6 # IB JB KB MCB 2 1 3 12 2 1 4 12 2 1 5 12 3 1 4 12 3 1 5 12 4 1 5 12 # 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 mtb43b1.dat SOL TYPE ZN2+ # 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 24 65 2.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # 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 mtb43b1.dat SOL TYPE NA+ # 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 34 23 1.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # 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 mtb43b1.dat SOL TYPE CL- # 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 35 35 -1.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # 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 mtb43b1.dat SOL TYPE CA2+ # 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 26 40 2.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # 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 mtb43b1.dat SOL TYPE MG2+ # 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 25 24 2.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # 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 mtb43b1.dat SOL TYPE CU1+ # building block (residue, nucleotide, etc.) # RNME CU1+ # number of atoms, number of preceding exclusions # NMAT NLIN 1 0 # atoms #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 CU 21 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 mtb43b1.dat SOL TYPE CU2+ # building block (residue, nucleotide, etc.) # RNME CU2+ # number of atoms, number of preceding exclusions # NMAT NLIN 1 0 # atoms #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 CU 22 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 mtb43b1.dat SOL TYPE H2O # 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 4 16 -0.82000 0 2 2 3 2 HW1 18 1 0.41000 0 1 3 3 HW2 18 1 0.41000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 3 # IB JB MCB 1 2 35 1 3 35 2 3 41 # 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 mtb43b1.dat SOL TYPE H2OE # 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 4 16 -0.84760 0 2 2 3 2 HW1 18 1 0.42380 0 1 3 3 HW2 18 1 0.42380 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 3 # IB JB MCB 1 2 35 1 3 35 2 3 41 # 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 mtb43b1.dat SOL TYPE CHCL3 # 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 36 12 0.17900 0 4 2 3 4 5 2 HChl 38 1 0.08200 0 3 3 4 5 3 CLCh1 37 35 -0.08700 0 2 4 5 4 CLCh2 37 35 -0.08700 0 1 5 5 CLCh3 37 35 -0.08700 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 9 # IB JB MCB 1 3 37 1 4 37 1 5 37 2 3 42 2 4 42 2 5 42 3 4 43 3 5 43 4 5 43 # 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 mtb43b1.dat SOL TYPE DMSO # 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 39 32 0.13900 0 3 2 3 4 2 ODmso 41 16 -0.45900 0 2 3 4 3 CDms1 40 5 0.16000 0 1 4 4 CDms2 40 5 0.16000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 6 # IB JB MCB 1 2 38 1 3 39 1 4 39 2 3 44 2 4 44 3 4 45 # 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 mtb43b1.dat SOL TYPE CH3OH # 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 33 16 -0.57400 0 2 2 3 2 HMet 18 1 0.39800 0 1 3 3 CMet 32 5 0.17600 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 3 # IB JB MCB 1 2 1 1 3 17 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 mtb43b1.dat SOL TYPE CCL4 # 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 42 12 0.00000 0 4 2 3 4 5 2 CLCl1 43 35 0.00000 0 3 3 4 5 3 CLCl2 43 35 0.00000 0 2 4 5 4 CLCl3 43 35 0.00000 0 1 5 5 CLCl4 43 35 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM # bonds # NB 9 # IB JB MCB 1 2 40 1 3 40 1 4 40 1 5 40 2 3 47 2 4 47 2 5 47 3 4 47 3 5 47 # 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 MTBUILDBLSOLVENT #@BLOCKTYPE mtb43b1.dat SVT TYPE H2O #solvent name #RNMES H2O #number of atoms 3 #atoms #ATOM ANM IAC MASS CG 1 OW 4 16 -.82 2 HW1 18 1 .41 3 HW2 18 1 .41 #constraints #number 3 # IB JB LENGTH 1 2 0.1 1 3 0.1 2 3 0.163299 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE mtb43b1.dat SVT TYPE H2OE #solvent name #RNMES H2OE #number of atoms 3 #atoms #ATOM ANM IAC MASS CG 1 OW 4 16 -.8476 2 HW1 18 1 .4238 3 HW2 18 1 .4238 #constraints #number 3 # IB JB LENGTH 1 2 0.1 1 3 0.1 2 3 0.163299 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE mtb43b1.dat SVT TYPE CHCL3 #solvent name #RNMES CHCL3 #number of atoms 5 #atoms #ATOM ANM IAC MASS CG 1 CChl 36 12 .179 2 HChl 38 1 .082 3 CLCh1 37 35 -.087 4 CLCh2 37 35 -.087 5 CLCh3 37 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 mtb43b1.dat SVT TYPE DMSO #solvent name #RNMES DMSO #number of atoms 4 #atoms #ATOM ANM IAC MASS CG 1 SDmso 39 32 .139 2 ODmso 41 16 -.459 3 CDms1 40 5 .16 4 CDms2 40 5 .16 #constraints #number 6 # IB JB LENGTH 1 2 0.153 1 3 0.195 1 4 0.195 2 3 0.280412 2 4 0.280412 3 4 0.292993 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE mtb43b1.dat SVT TYPE CH3OH #solvent name #RNMES CH3OH #number of atoms 3 #atoms #ATOM ANM IAC MASS CG 1 OMet 33 16 -.574 2 HMet 18 1 .398 3 CMet 32 5 .176 #constraints #number 3 # IB JB LENGTH 1 2 0.1000 1 3 0.1430 2 3 0.198842 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE mtb43b1.dat SVT TYPE CCL4 #solvent name #RNMES CCL4 #number of atoms 5 #atoms #ATOM ANM IAC MASS CG 1 CCl4 42 12 .0 2 CLCl1 43 35 .0 3 CLCl2 43 35 .0 4 CLCl3 43 35 .0 5 CLCl4 43 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