TITLE File : mtb45a4.dat Force field : 45A4 (condensed-phase simulations) Reference : Soares et al. J. Comput. Chem. 2005, 26, 725-737; Lins & Hunenberger J. Comput. Chem. 2005, 26, 1400-1412 File content : molecular topology building blocks (alpha amino acids, nucleic acids, lipids) Format : GROMOS96 Initial file : WFVG, PHH, CO, Zuerich, 2006 Time stamp : PHH, Thu Nov 10 21:47:55 CET 2011 Remark : Changes from 45A(B)3 are extensive and affect the nucleotides, carbohydrates, lipids and heme Remark : DG, CO, NS, PHH, Jan 2008, following adaptations/corrections were made: - Explicit aromatic hydrogens were added - Dihedral type 22 added to P-O5*-C5*-C4* in nucleotides and cofactors - Exclusion error in URA was corrected - Small errors were corrected in cofactors CYT*, DHF, THF, TMP, TMPH, TMPHP - Exclusion errors in HEME and HEMC cofactors were corrected - A RNA Capping group was added (3OH) - A small error in the charge distribution in NH2 was corrected - Carbohydrates were added Remark : The above changes are propagated to subsequent force-field versions 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: Changed atom name H3 by H2 in NH2 patch. PHH, 09.11.2011: Introduced a copy of patch D5OH named 5OH, the latter meant for RNA instead of DNA. END FORCEFIELD 45A4 END TOPPHYSCON # FPEPSI: 1.0/(4.0*PI*EPS0) (EPS0 is the permittivity of vacuum) 0.1389354E+03 # HBAR: Planck's constant HBAR = H/(2* PI) 0.6350780E-01 END LINKEXCLUSIONS #nearest neighbour exclusions when linking #NRNE 2 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 0.09000 0 3 7 8 9 7 NE 10 14 -0.11000 0 4 8 9 10 13 8 HE 18 1 0.24000 0 1 9 9 CZ 11 12 0.34000 0 6 10 11 12 13 14 15 10 NH1 9 14 -0.26000 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 -0.26000 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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 0.27000 0 2 6 7 6 OD1 2 16 -0.63500 0 1 7 7 OD2 2 16 -0.63500 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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 -0.10000 0 2 5 6 5 SG 20 32 -0.40000 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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 0.27000 0 2 7 8 7 OE1 2 16 -0.63500 0 1 8 8 OE2 2 16 -0.63500 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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 -0.05000 0 6 6 7 8 9 10 11 6 ND1 8 14 0.38000 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 -0.24000 0 2 10 11 10 NE2 8 14 0.31000 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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.dat SOL TYPE HIS1 # building block (residue, nucleotide, etc.) # RNME HIS1 # # Histidine covalently bound to HEME group # # 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 -1 6 7 8 9 10 6 ND1 8 14 0.00000 0 5 -1 7 8 9 10 7 HD1 18 1 0.19000 0 3 8 9 10 8 CD2 16 3 0.13000 0 3 -1 9 10 9 CE1 16 3 0.26000 0 2 -1 10 10 NE2 8 14 -0.58000 1 5 -5 -4 -3 -2 -1 # 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 4 26 3 11 26 4 5 26 5 6 9 5 8 9 6 7 2 6 9 9 8 10 9 9 10 9 11 12 4 11 13 9 -1 10 48 # bond angles # NBA 25 # IB JB KB MCB -1 1 2 31 -1 1 3 30 2 1 3 17 1 3 4 12 1 3 11 12 4 3 11 12 3 4 5 14 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 -1 10 8 33 -1 10 9 33 -2 -1 10 1 -3 -1 10 1 -4 -1 10 1 -5 -1 10 1 8 10 9 6 3 11 12 29 3 11 13 18 12 11 13 32 # improper dihedrals # NIDA 10 # IB JB KB LB MCB 1 -1 3 2 1 3 1 11 4 2 5 6 8 4 1 5 6 9 10 1 5 8 10 9 1 6 5 8 10 1 6 5 9 7 1 6 9 10 8 1 8 5 6 9 1 11 3 13 12 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 11 19 1 3 4 5 17 1 3 11 13 20 3 4 5 6 20 -2 -1 10 8 18 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.dat SOL TYPE HIS2 # building block (residue, nucleotide, etc.) # RNME HIS2 # # Histidine covalently bound to HEME group to be used if a sixth ligand is bound to FE # # 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 -1 6 7 8 9 10 6 ND1 8 14 0.00000 0 5 -1 7 8 9 10 7 HD1 18 1 0.19000 0 3 8 9 10 8 CD2 16 3 0.13000 0 3 -1 9 10 9 CE1 16 3 0.26000 0 2 -1 10 10 NE2 8 14 -0.58000 1 6 -5 -4 -3 -2 -1 -48 # 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 4 26 3 11 26 4 5 26 5 6 9 5 8 9 6 7 2 6 9 9 8 10 9 9 10 9 11 12 4 11 13 9 -1 10 48 # bond angles # NBA 25 # IB JB KB MCB -1 1 2 31 -1 1 3 30 2 1 3 17 1 3 4 12 1 3 11 12 4 3 11 12 3 4 5 14 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 -1 10 8 33 -1 10 9 33 -2 -1 10 1 -3 -1 10 1 -4 -1 10 1 -5 -1 10 1 8 10 9 6 3 11 12 29 3 11 13 18 12 11 13 32 # improper dihedrals # NIDA 10 # IB JB KB LB MCB 1 -1 3 2 1 3 1 11 4 2 5 6 8 4 1 5 6 9 10 1 5 8 10 9 1 6 5 8 10 1 6 5 9 7 1 6 9 10 8 1 8 5 6 9 1 11 3 13 12 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 4 -1 1 3 11 19 1 3 4 5 17 1 3 11 13 20 3 4 5 6 20 -2 -1 10 8 18 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 44 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 44 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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 0.12700 0 4 8 9 10 11 8 NZ 7 14 0.12900 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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 44 4 0.00000 1 3 4 5 6 4 CG 44 4 0.00000 0 1 5 5 CD 44 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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.dat SOL TYPE DADE # building block (residue, nucleotide, etc.) # RNME DADE # NMAT NLIN 25 2 #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 27 31 0.99 0 4 2 3 4 5 2 O1P 2 16 -0.635 0 2 3 4 3 O2P 2 16 -0.635 0 1 4 4 O5* 3 16 -0.36 1 2 5 6 5 C5* 13 4 0 1 3 6 7 24 6 C4* 12 3 0.16 0 5 7 8 23 24 25 7 O4* 3 16 -0.36 0 4 8 9 23 24 8 C1* 12 3 0.2 1 9 9 10 11 19 20 21 22 23 24 9 N9 8 14 -0.2 0 9 10 11 12 15 19 20 21 22 23 10 C4 11 12 0.2 1 10 11 12 13 14 15 16 19 20 21 22 11 N3 8 14 -0.54 0 7 12 13 14 15 19 20 21 12 C2 11 12 0.44 0 5 13 14 15 16 19 13 H2 17 1 0.1 1 2 14 15 14 N1 8 14 -0.54 0 4 15 16 19 20 15 C6 11 12 0.54 1 6 16 17 18 19 20 21 16 N6 6 14 -0.83 0 4 17 18 19 20 # N7 is excluded from H61 and H62 to prevent shake failures 17 H61 18 1 0.415 0 2 18 20 18 H62 18 1 0.415 1 1 20 19 C5 11 12 0 0 3 20 21 22 20 N7 8 14 -0.54 0 2 21 22 21 C8 11 12 0.44 0 1 22 22 H8 17 1 0.1 1 0 23 C2* 44 4 0 0 2 24 25 24 C3* 12 3 0 1 25 O3* 3 16 -0.36 0 # 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 9 10 9 9 21 9 10 11 11 10 19 15 11 12 6 12 13 3 12 14 6 14 15 11 15 16 8 15 19 15 16 17 2 16 18 2 19 20 9 20 21 9 21 22 3 23 24 25 24 25 19 25 26 27 # 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 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 21 36 10 9 21 6 9 10 11 38 9 10 19 6 11 10 19 26 10 11 12 26 11 12 13 24 11 12 14 26 13 12 14 24 12 14 15 26 14 15 16 26 14 15 19 26 16 15 19 26 15 16 17 22 15 16 18 22 17 16 18 23 10 19 15 26 10 19 20 6 15 19 20 38 19 20 21 6 9 21 20 6 9 21 22 35 20 21 22 35 8 23 24 7 6 24 23 7 6 24 25 8 23 24 25 8 24 25 26 25 # NIDA 21 # IB JB KB LB MCB 8 10 21 9 1 9 10 19 20 1 10 9 11 19 1 10 9 21 20 1 10 11 12 14 1 10 19 20 21 1 11 10 19 15 1 11 12 14 15 1 12 14 15 19 1 12 11 13 14 1 14 15 19 10 1 16 14 19 15 1 16 17 18 15 1 19 10 11 12 1 19 15 20 10 1 19 20 21 9 1 21 9 10 19 1 21 9 20 22 1 23 7 9 8 2 24 5 7 6 2 24 23 25 6 2 # NDA 23 # IB JB KB LB MCB -1 0 1 4 24 -1 0 1 4 25 0 1 4 5 24 0 1 4 5 25 1 4 5 6 26 1 4 5 6 11 4 5 6 7 22 4 5 6 7 23 4 5 6 24 7 4 5 6 24 17 24 6 7 8 14 5 6 24 23 17 5 6 24 25 7 7 6 24 23 7 7 6 24 25 8 6 7 8 23 14 7 8 9 10 6 7 8 23 24 7 7 8 23 24 17 19 15 16 17 4 8 23 24 6 17 8 23 24 25 7 6 24 25 26 14 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.dat SOL TYPE DGUA # building block (residue, nucleotide, etc.) # RNME DGUA # NMAT NLIN 26 2 #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 27 31 0.99 0 4 2 3 4 5 2 O1P 2 16 -0.635 0 2 3 4 3 O2P 2 16 -0.635 0 1 4 4 O5* 3 16 -0.36 1 2 5 6 5 C5* 13 4 0 1 3 6 7 25 6 C4* 12 3 0.16 0 5 7 8 24 25 26 7 O4* 3 16 -0.36 0 4 8 9 24 25 8 C1* 12 3 0.2 1 9 9 10 11 20 21 22 23 24 25 9 N9 8 14 -0.2 0 9 10 11 12 18 20 21 22 23 24 10 C4 11 12 0.2 1 10 11 12 13 16 18 19 20 21 22 23 11 N3 8 14 -0.54 0 8 12 13 16 17 18 20 21 22 12 C2 11 12 0.54 1 8 13 14 15 16 17 18 19 20 13 N2 6 14 -0.83 0 5 14 15 16 17 18 14 H21 18 1 0.415 0 1 15 15 H22 18 1 0.415 1 0 16 N1 8 14 -0.31 0 5 17 18 19 20 21 17 H1 18 1 0.31 1 3 18 19 20 18 C6 11 12 0.45 0 4 19 20 21 22 19 O6 1 16 -0.45 1 2 20 21 20 C5 11 12 0 0 3 21 22 23 21 N7 8 14 -0.54 0 2 22 23 22 C8 11 12 0.44 0 1 23 23 H8 17 1 0.10 1 0 24 C2* 44 4 0 0 2 25 26 25 C3* 12 3 0 1 26 O3* 3 16 -0.36 0 # NB 29 # IB JB MCB 1 2 23 1 3 23 1 4 27 4 5 19 5 6 25 6 7 19 6 25 25 7 8 19 8 9 21 8 24 25 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 16 18 16 18 19 4 18 20 15 20 21 9 21 22 9 22 23 3 24 25 25 25 26 19 26 27 27 # NBA 46 # 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 25 7 7 6 25 8 6 7 8 9 7 8 9 8 7 8 24 8 9 8 24 8 8 9 10 36 8 9 22 36 10 9 22 6 9 10 11 38 9 10 20 6 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 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 9 22 23 35 21 22 23 35 8 24 25 7 6 25 24 7 6 25 26 8 24 25 26 8 25 26 27 25 # NIDA 22 # IB JB KB LB MCB 8 10 22 9 1 9 10 20 21 1 10 9 11 20 1 10 9 22 21 1 10 11 12 16 1 10 20 21 22 1 11 10 20 18 1 11 12 16 18 1 12 16 18 20 1 13 11 16 12 1 13 14 15 12 1 16 18 20 10 1 17 12 18 16 1 19 16 20 18 1 20 10 11 12 1 20 18 21 10 1 20 21 22 9 1 22 9 10 20 1 22 9 21 23 1 24 7 9 8 2 25 5 7 6 2 25 24 26 6 2 # NDA 23 # IB JB KB LB MCB -1 0 1 4 24 -1 0 1 4 25 0 1 4 5 24 0 1 4 5 25 1 4 5 6 26 1 4 5 6 11 4 5 6 7 22 4 5 6 7 23 4 5 6 25 7 4 5 6 25 17 25 6 7 8 14 5 6 25 24 17 5 6 25 26 7 7 6 25 24 7 7 6 25 26 8 6 7 8 24 14 7 8 9 10 6 7 8 24 25 7 7 8 24 25 17 11 12 13 14 4 8 24 25 6 17 8 24 25 26 7 6 25 26 27 14 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.dat SOL TYPE DCYT # building block (residue, nucleotide, etc.) # RNME DCYT # NMAT NLIN 23 2 #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 27 31 0.99 0 4 2 3 4 5 2 O1P 2 16 -0.635 0 2 3 4 3 O2P 2 16 -0.635 0 1 4 4 O5* 3 16 -0.36 1 2 5 6 5 C5* 13 4 0 1 3 6 7 22 6 C4* 12 3 0.16 0 5 7 8 21 22 23 7 O4* 3 16 -0.36 0 4 8 9 21 22 8 C1* 12 3 0.2 1 9 9 10 11 12 13 14 19 21 22 9 N1 8 14 -0.2 0 9 10 11 12 13 14 15 19 20 21 10 C6 11 12 0.1 0 8 11 12 13 14 15 16 19 20 11 H6 17 1 0.1 1 4 12 15 19 20 12 C2 11 12 0.45 0 5 13 14 15 16 19 13 O2 1 16 -0.45 1 2 14 15 14 N3 8 14 -0.54 0 4 15 16 19 20 15 C4 11 12 0.54 1 5 16 17 18 19 20 16 N4 6 14 -0.83 0 4 17 18 19 20 17 H41 18 1 0.415 0 1 18 18 H42 18 1 0.415 1 0 19 C5 11 12 -0.1 0 1 20 20 H5 17 1 0.1 1 0 21 C2* 44 4 0 0 2 22 23 22 C3* 12 3 0 1 23 O3* 3 16 -0.36 0 # 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 21 25 9 10 16 9 12 16 10 11 3 10 19 15 12 13 4 12 14 11 14 15 11 15 16 8 15 19 15 16 17 2 16 18 2 19 20 3 21 22 25 22 23 19 23 24 27 # NBA 39 # 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 7 6 22 8 6 7 8 9 7 8 9 8 7 8 21 8 9 8 21 7 8 9 10 26 8 9 12 26 10 9 12 26 9 10 11 24 9 10 19 26 11 10 19 24 9 12 13 26 9 12 14 26 13 12 14 26 12 14 15 26 14 15 16 26 14 15 19 26 16 15 19 26 15 16 17 22 15 16 18 22 17 16 18 23 10 19 15 26 10 19 20 24 15 19 20 24 8 21 22 7 6 22 21 7 6 22 23 8 21 22 23 8 22 23 24 25 # NIDA 15 # IB JB KB LB MCB 9 10 12 8 1 9 10 19 15 1 9 12 14 15 1 10 9 12 14 1 10 9 19 11 1 12 9 10 19 1 12 14 15 19 1 13 9 14 12 1 14 15 19 10 1 16 14 19 15 1 16 17 18 15 1 19 10 15 20 1 21 7 9 8 2 22 5 7 6 2 22 21 23 6 2 # NDA 23 # IB JB KB LB MCB -1 0 1 4 24 -1 0 1 4 25 0 1 4 5 24 0 1 4 5 25 1 4 5 6 26 1 4 5 6 11 4 5 6 7 22 4 5 6 7 23 4 5 6 22 7 4 5 6 22 17 22 6 7 8 14 5 6 22 21 17 5 6 22 23 7 7 6 22 21 7 7 6 22 23 8 6 7 8 21 14 7 8 9 12 6 7 8 21 22 7 7 8 21 22 17 14 15 16 17 4 8 21 22 6 17 8 21 22 23 7 6 22 23 24 14 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.dat SOL TYPE DTHY # building block (residue, nucleotide, etc.) # RNME DTHY # NMAT NLIN 22 2 #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 27 31 0.99 0 4 2 3 4 5 2 O1P 2 16 -0.635 0 2 3 4 3 O2P 2 16 -0.635 0 1 4 4 O5* 3 16 -0.36 1 2 5 6 5 C5* 13 4 0 1 3 6 7 21 6 C4* 12 3 0.16 0 5 7 8 20 21 22 7 O4* 3 16 -0.36 0 4 8 9 20 21 8 C1* 12 3 0.2 1 9 9 10 11 12 13 14 18 20 21 9 N1 8 14 -0.2 0 10 10 11 12 13 14 15 16 18 19 20 10 C6 11 12 0.1 0 8 11 12 13 14 16 17 18 19 11 H6 17 1 0.1 1 4 12 16 18 19 12 C2 11 12 0.45 0 6 13 14 15 16 17 18 13 O2 1 16 -0.45 1 3 14 15 16 14 N3 8 14 -0.31 0 5 15 16 17 18 19 15 H3 18 1 0.31 1 3 16 17 18 16 C4 11 12 0.45 0 3 17 18 19 17 O4 1 16 -0.45 1 2 18 19 18 C5 11 12 0 0 1 19 19 C5M 14 5 0 1 0 20 C2* 44 4 0 0 2 21 22 21 C3* 12 3 0 1 22 O3* 3 16 -0.36 0 # 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 20 25 9 10 16 9 12 16 10 11 3 10 18 15 12 13 4 12 14 16 14 15 2 14 16 16 16 17 4 16 18 15 18 19 26 20 21 25 21 22 19 22 23 27 # 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 21 7 7 6 21 8 6 7 8 9 7 8 9 8 7 8 20 8 9 8 20 7 8 9 10 26 8 9 12 26 10 9 12 26 9 10 11 24 9 10 18 26 11 10 18 24 9 12 13 26 9 12 14 26 13 12 14 26 12 14 15 24 12 14 16 26 15 14 16 24 14 16 17 26 14 16 18 26 17 16 18 26 10 18 16 26 10 18 19 26 16 18 19 26 8 20 21 7 6 21 20 7 6 21 22 8 20 21 22 8 21 22 23 25 # NIDA 15 # IB JB KB LB MCB 9 10 12 8 1 9 10 18 16 1 9 12 14 16 1 10 9 12 14 1 10 9 18 11 1 12 9 10 18 1 12 14 16 18 1 13 9 14 12 1 14 16 18 10 1 15 12 16 14 1 17 14 18 16 1 18 10 16 19 1 20 7 9 8 2 21 5 7 6 2 21 20 22 6 2 # NDA 22 # IB JB KB LB MCB -1 0 1 4 24 -1 0 1 4 25 0 1 4 5 24 0 1 4 5 25 1 4 5 6 26 1 4 5 6 11 4 5 6 7 22 4 5 6 7 23 4 5 6 21 7 4 5 6 21 17 21 6 7 8 14 5 6 21 20 17 5 6 21 22 7 7 6 21 20 7 7 6 21 22 8 6 7 8 20 14 7 8 9 12 6 7 8 20 21 7 7 8 20 21 17 8 20 21 6 17 8 20 21 22 7 6 21 22 23 14 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.dat SOL TYPE ADE # building block (residue, nucleotide, etc.) # RNME ADE # NMAT NLIN 27 2 #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 27 31 0.99 0 4 2 3 4 5 2 O1P 2 16 -0.635 0 2 3 4 3 O2P 2 16 -0.635 0 1 4 4 O5* 3 16 -0.36 1 2 5 6 5 C5* 13 4 0 1 3 6 7 26 6 C4* 12 3 0.16 0 5 7 8 23 26 27 7 O4* 3 16 -0.36 0 4 8 9 23 26 8 C1* 12 3 0.2 1 10 9 10 11 19 20 21 22 23 24 26 9 N9 8 14 -0.2 0 9 10 11 12 15 19 20 21 22 23 10 C4 11 12 0.2 1 10 11 12 13 14 15 16 19 20 21 22 11 N3 8 14 -0.54 0 7 12 13 14 15 19 20 21 12 C2 11 12 0.44 0 5 13 14 15 16 19 13 H2 17 1 0.1 1 2 14 15 14 N1 8 14 -0.54 0 4 15 16 19 20 15 C6 11 12 0.54 1 6 16 17 18 19 20 21 16 N6 6 14 -0.83 0 4 17 18 19 20 17 H61 18 1 0.415 0 2 18 20 18 H62 18 1 0.415 1 1 20 19 C5 11 12 0 0 3 20 21 22 20 N7 8 14 -0.54 0 2 21 22 21 C8 11 12 0.44 0 1 22 22 H8 17 1 0.1 1 0 23 C2* 12 3 0.15 0 4 24 25 26 27 24 O2* 3 16 -0.548 0 2 25 26 25 H2* 18 1 0.398 1 0 26 C3* 12 3 0 1 27 O3* 3 16 -0.36 0 # 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 9 10 9 9 21 9 10 11 11 10 19 15 11 12 6 12 13 3 12 14 6 14 15 11 15 16 8 15 19 15 16 17 2 16 18 2 19 20 9 20 21 9 21 22 3 23 24 19 23 26 25 24 25 1 26 27 19 27 28 27 # 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 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 21 36 10 9 21 6 9 10 11 38 9 10 19 6 11 10 19 26 10 11 12 26 11 12 13 24 11 12 14 26 13 12 14 24 12 14 15 26 14 15 16 26 14 15 19 26 16 15 19 26 15 16 17 22 15 16 18 22 17 16 18 23 10 19 15 26 10 19 20 6 15 19 20 38 19 20 21 6 9 21 20 6 9 21 22 35 20 21 22 35 8 23 24 8 8 23 26 7 24 23 26 8 23 24 25 11 6 26 23 7 6 26 27 8 23 26 27 8 26 27 28 25 # NIDA 22 # IB JB KB LB MCB 8 10 21 9 1 9 10 19 20 1 10 9 11 19 1 10 9 21 20 1 10 11 12 14 1 10 19 20 21 1 11 10 19 15 1 11 12 14 15 1 12 11 13 14 1 12 14 15 19 1 14 15 19 10 1 16 14 19 15 1 16 17 18 15 1 19 10 11 12 1 19 15 20 10 1 19 20 21 9 1 21 9 10 19 1 21 9 20 22 1 23 7 9 8 2 23 24 26 8 2 26 5 7 6 2 26 23 27 6 2 # NDA 28 # IB JB KB LB MCB -1 0 1 4 24 -1 0 1 4 25 0 1 4 5 24 0 1 4 5 25 1 4 5 6 26 1 4 5 6 11 4 5 6 7 22 4 5 6 7 23 4 5 6 26 7 4 5 6 26 17 26 6 7 8 14 5 6 26 23 17 5 6 26 27 7 7 6 26 23 7 7 6 26 27 8 6 7 8 23 14 7 8 9 10 6 7 8 23 24 8 7 8 23 26 7 7 8 23 26 17 9 8 23 24 7 19 15 16 17 4 8 23 24 25 12 8 23 26 6 17 8 23 26 27 7 24 23 26 6 7 24 23 26 27 8 6 26 27 28 14 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.dat SOL TYPE GUA # building block (residue, nucleotide, etc.) # RNME GUA # NMAT NLIN 28 2 #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 27 31 0.99 0 4 2 3 4 5 2 O1P 2 16 -0.635 0 2 3 4 3 O2P 2 16 -0.635 0 1 4 4 O5* 3 16 -0.36 1 2 5 6 5 C5* 13 4 0 1 3 6 7 27 6 C4* 12 3 0.16 0 5 7 8 24 27 28 7 O4* 3 16 -0.36 0 4 8 9 24 27 8 C1* 12 3 0.2 1 10 9 10 11 20 21 22 23 24 25 27 9 N9 8 14 -0.2 0 9 10 11 12 18 20 21 22 23 24 10 C4 11 12 0.2 1 10 11 12 13 16 18 19 20 21 22 23 11 N3 8 14 -0.54 0 8 12 13 16 17 18 20 21 22 12 C2 11 12 0.54 1 8 13 14 15 16 17 18 19 20 13 N2 6 14 -0.83 0 5 14 15 16 17 18 14 H21 18 1 0.415 0 1 15 15 H22 18 1 0.415 1 0 16 N1 8 14 -0.31 0 5 17 18 19 20 21 17 H1 18 1 0.31 1 3 18 19 20 18 C6 11 12 0.45 0 4 19 20 21 22 19 O6 1 16 -0.45 1 2 20 21 20 C5 11 12 0 0 3 21 22 23 21 N7 8 14 -0.54 0 2 22 23 22 C8 11 12 0.44 0 1 23 23 H8 17 1 0.1 1 0 24 C2* 12 3 0.15 0 4 25 26 27 28 25 O2* 3 16 -0.548 0 2 26 27 26 H2* 18 1 0.398 1 0 27 C3* 12 3 0 1 28 O3* 3 16 -0.36 0 # NB 31 # IB JB MCB 1 2 23 1 3 23 1 4 27 4 5 19 5 6 25 6 7 19 6 27 25 7 8 19 8 9 21 8 24 25 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 16 18 16 18 19 4 18 20 15 20 21 9 21 22 9 22 23 3 24 25 19 24 27 25 25 26 1 27 28 19 28 29 27 # NBA 49 # 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 27 7 7 6 27 8 6 7 8 9 7 8 9 8 7 8 24 8 9 8 24 8 8 9 10 36 8 9 22 36 10 9 22 6 9 10 11 38 9 10 20 6 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 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 9 22 23 35 21 22 23 35 8 24 25 8 8 24 27 7 25 24 27 8 24 25 26 11 6 27 24 7 6 27 28 8 24 27 28 8 27 28 29 25 # NIDA 23 # IB JB KB LB MCB 8 10 22 9 1 9 10 20 21 1 10 9 11 20 1 10 9 22 21 1 10 11 12 16 1 10 20 21 22 1 11 10 20 18 1 11 12 16 18 1 12 16 18 20 1 13 11 16 12 1 13 14 15 12 1 16 18 20 10 1 17 12 18 16 1 19 16 20 18 1 20 10 11 12 1 20 18 21 10 1 20 21 22 9 1 22 9 10 20 1 22 9 21 23 1 24 7 9 8 2 24 25 27 8 2 27 5 7 6 2 27 24 28 6 2 # NDA 28 # IB JB KB LB MCB -1 0 1 4 24 -1 0 1 4 25 0 1 4 5 24 0 1 4 5 25 1 4 5 6 26 1 4 5 6 11 4 5 6 7 22 4 5 6 7 23 4 5 6 27 7 4 5 6 27 17 27 6 7 8 14 5 6 27 24 17 5 6 27 28 7 7 6 27 24 7 7 6 27 28 8 6 7 8 24 14 7 8 9 10 6 7 8 24 25 8 7 8 24 27 7 7 8 24 27 17 9 8 24 25 7 11 12 13 14 4 8 24 25 26 12 8 24 27 6 17 8 24 27 28 7 25 24 27 6 7 25 24 27 28 8 6 27 28 29 14 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.dat SOL TYPE CYT # building block (residue, nucleotide, etc.) # RNME CYT # NMAT NLIN 25 2 #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 27 31 0.99 0 4 2 3 4 5 2 O1P 2 16 -0.635 0 2 3 4 3 O2P 2 16 -0.635 0 1 4 4 O5* 3 16 -0.36 1 2 5 6 5 C5* 13 4 0 1 3 6 7 24 6 C4* 12 3 0.16 0 5 7 8 21 24 25 7 O4* 3 16 -0.36 0 4 8 9 21 24 8 C1* 12 3 0.2 1 10 9 10 11 12 13 14 19 21 22 24 9 N1 8 14 -0.2 0 9 10 11 12 13 14 15 19 20 21 10 C6 11 12 0.1 0 8 11 12 13 14 15 16 19 20 11 H6 17 1 0.1 1 4 12 15 19 20 12 C2 11 12 0.45 0 5 13 14 15 16 19 13 O2 1 16 -0.45 1 2 14 15 14 N3 8 14 -0.54 0 4 15 16 19 20 15 C4 11 12 0.54 1 5 16 17 18 19 20 16 N4 6 14 -0.83 0 4 17 18 19 20 17 H41 18 1 0.415 0 1 18 18 H42 18 1 0.415 1 0 19 C5 11 12 -0.1 0 1 20 20 H5 17 1 0.1 1 0 21 C2* 12 3 0.15 0 4 22 23 24 25 22 O2* 3 16 -0.548 0 2 23 24 23 H2* 18 1 0.398 1 0 24 C3* 12 3 0 1 25 O3* 3 16 -0.36 0 # NB 27 # 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 22 8 21 25 9 10 16 9 12 16 10 11 3 10 19 15 12 13 4 12 14 11 14 15 11 15 16 8 15 19 15 16 17 2 16 18 2 19 20 3 21 22 19 21 24 25 22 23 1 24 25 19 25 26 27 # NBA 42 # 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 7 6 24 8 6 7 8 9 7 8 9 8 7 8 21 8 9 8 21 7 8 9 10 26 8 9 12 26 10 9 12 26 9 10 11 24 9 10 19 26 11 10 19 24 9 12 13 26 9 12 14 26 13 12 14 26 12 14 15 26 14 15 16 26 14 15 19 26 16 15 19 26 15 16 17 22 15 16 18 22 17 16 18 23 10 19 15 26 10 19 20 24 15 19 20 24 8 21 22 8 8 21 24 7 22 21 24 8 21 22 23 11 6 24 21 7 6 24 25 8 21 24 25 8 24 25 26 25 # NIDA 16 # IB JB KB LB MCB 9 10 12 8 1 9 10 19 15 1 9 12 14 15 1 10 9 12 14 1 10 9 19 11 1 12 9 10 19 1 12 14 15 19 1 13 9 14 12 1 14 15 19 10 1 16 14 19 15 1 16 17 18 15 1 19 10 15 20 1 21 7 9 8 2 21 22 24 8 2 24 5 7 6 2 24 21 25 6 2 # NDA 28 # IB JB KB LB MCB -1 0 1 4 24 -1 0 1 4 25 0 1 4 5 24 0 1 4 5 25 1 4 5 6 26 1 4 5 6 11 4 5 6 7 22 4 5 6 7 23 4 5 6 24 7 4 5 6 24 17 24 6 7 8 14 5 6 24 21 17 5 6 24 25 7 7 6 24 21 7 7 6 24 25 8 6 7 8 21 14 7 8 9 12 6 7 8 21 22 8 7 8 21 24 7 7 8 21 24 17 9 8 21 22 7 14 15 16 17 4 8 21 22 23 12 8 21 24 6 17 8 21 24 25 7 22 21 24 6 7 22 21 24 25 8 6 24 25 26 14 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.dat SOL TYPE URA # building block (residue, nucleotide, etc.) # RNME URA # NMAT NLIN 24 2 #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 27 31 0.99 0 4 2 3 4 5 2 O1P 2 16 -0.635 0 2 3 4 3 O2P 2 16 -0.635 0 1 4 4 O5* 3 16 -0.36 1 2 5 6 5 C5* 13 4 0 1 3 6 7 23 6 C4* 12 3 0.16 0 5 7 8 20 23 24 7 O4* 3 16 -0.36 0 4 8 9 20 23 8 C1* 12 3 0.2 1 10 9 10 11 12 13 14 18 20 21 23 9 N1 8 14 -0.2 0 10 10 11 12 13 14 15 16 18 19 20 10 C6 11 12 0.1 0 8 11 12 13 14 16 17 18 19 11 H6 17 1 0.1 1 4 12 16 18 19 12 C2 11 12 0.45 0 6 13 14 15 16 17 18 13 O2 1 16 -0.45 1 3 14 15 16 14 N3 8 14 -0.31 0 5 15 16 17 18 19 15 H3 18 1 0.31 1 3 16 17 18 16 C4 11 12 0.45 0 3 17 18 19 17 O4 1 16 -0.45 1 2 18 19 18 C5 11 12 -0.1 0 1 19 19 H5 17 1 0.1 1 0 20 C2* 12 3 0.15 0 4 21 22 23 24 21 O2* 3 16 -0.548 0 2 22 23 22 H2* 18 1 0.398 1 0 23 C3* 12 3 0 1 24 O3* 3 16 -0.36 0 # NB 26 # IB JB MCB 1 2 23 1 3 23 1 4 27 4 5 19 5 6 25 6 7 19 6 23 25 7 8 19 8 9 22 8 20 25 9 10 16 9 12 16 10 11 3 10 18 15 12 13 4 12 14 16 14 15 2 14 16 16 16 17 4 16 18 15 18 19 3 20 21 19 20 23 25 21 22 1 23 24 19 24 25 27 # NBA 41 # 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 23 7 7 6 23 8 6 7 8 9 7 8 9 8 7 8 20 8 9 8 20 7 8 9 10 26 8 9 12 26 10 9 12 26 9 10 11 24 9 10 18 26 11 10 18 24 9 12 13 26 9 12 14 26 13 12 14 26 12 14 15 24 12 14 16 26 15 14 16 24 14 16 17 26 14 16 18 26 17 16 18 26 10 18 16 26 10 18 19 24 16 18 19 24 8 20 21 8 8 20 23 7 21 20 23 8 20 21 22 11 6 23 20 7 6 23 24 8 20 23 24 8 23 24 25 25 # NIDA 16 # IB JB KB LB MCB 9 10 12 8 1 9 10 18 16 1 9 12 14 16 1 10 9 12 14 1 10 9 18 11 1 12 9 10 18 1 12 14 16 18 1 13 9 14 12 1 14 16 18 10 1 15 12 16 14 1 17 14 18 16 1 18 10 16 19 1 20 7 9 8 2 20 21 23 8 2 23 5 7 6 2 23 20 24 6 2 # NDA 27 # IB JB KB LB MCB -1 0 1 4 24 -1 0 1 4 25 0 1 4 5 24 0 1 4 5 25 1 4 5 6 26 1 4 5 6 11 4 5 6 7 22 4 5 6 7 23 4 5 6 23 7 4 5 6 23 17 23 6 7 8 14 5 6 23 20 17 5 6 23 24 7 7 6 23 20 7 7 6 23 24 8 6 7 8 20 14 7 8 9 12 6 7 8 20 21 8 7 8 20 23 7 7 8 20 23 17 9 8 20 21 7 8 20 21 22 12 8 20 23 6 17 8 20 23 24 7 21 20 23 6 7 21 20 23 24 8 6 23 24 25 14 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.dat SOL TYPE DPPC # building block (residue, nucleotide, etc.) # RNME DPPC # Dipalmitoylphosphatidylcholine # # number of atoms, number of preceding exclusions # NMAT NLIN 50 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C33 14 5 0.25000 0 4 2 3 4 5 2 C34 14 5 0.25000 0 3 3 4 5 3 C35 14 5 0.25000 0 2 4 5 4 N 7 14 0.00000 0 2 5 6 5 C32 13 4 0.25000 1 2 6 7 6 C31 13 4 0.00000 1 2 7 8 7 O32 3 16 -0.36000 0 4 8 9 10 11 8 P 27 31 0.99000 0 4 9 10 11 12 9 O33 2 16 -0.63500 0 2 10 11 10 O34 2 16 -0.63500 0 1 11 11 O31 3 16 -0.36000 1 2 12 13 12 C3 13 4 0.00000 1 3 13 14 32 13 C2 12 3 0.16000 0 4 14 15 32 33 14 O21 3 16 -0.36000 0 4 15 16 17 32 15 C21 11 12 0.58000 0 3 16 17 18 16 O22 1 16 -0.38000 1 1 17 17 C22 13 4 0.00000 0 2 18 19 18 C23 13 4 0.00000 1 2 19 20 19 C24 13 4 0.00000 0 2 20 21 20 C25 13 4 0.00000 1 2 21 22 21 C26 13 4 0.00000 0 2 22 23 22 C27 13 4 0.00000 1 2 23 24 23 C28 13 4 0.00000 0 2 24 25 24 C29 13 4 0.00000 1 2 25 26 25 C210 13 4 0.00000 0 2 26 27 26 C211 13 4 0.00000 1 2 27 28 27 C212 13 4 0.00000 0 2 28 29 28 C213 13 4 0.00000 1 2 29 30 29 C214 13 4 0.00000 0 2 30 31 30 C215 13 4 0.00000 1 1 31 31 C216 14 5 0.00000 1 0 32 C1 13 4 0.16000 0 2 33 34 33 O11 3 16 -0.36000 0 3 34 35 36 34 C11 11 12 0.58000 0 3 35 36 37 35 O12 1 16 -0.38000 1 1 36 36 C12 13 4 0.00000 0 2 37 38 37 C13 13 4 0.00000 1 2 38 39 38 C14 13 4 0.00000 0 2 39 40 39 C15 13 4 0.00000 1 2 40 41 40 C16 13 4 0.00000 0 2 41 42 41 C17 13 4 0.00000 1 2 42 43 42 C18 13 4 0.00000 0 2 43 44 43 C19 13 4 0.00000 1 2 44 45 44 C110 13 4 0.00000 0 2 45 46 45 C111 13 4 0.00000 1 2 46 47 46 C112 13 4 0.00000 0 2 47 48 47 C113 13 4 0.00000 1 2 48 49 48 C114 13 4 0.00000 0 2 49 50 49 C115 13 4 0.00000 1 1 50 50 C116 14 5 0.00000 1 0 # bonds # NB 49 # IB JB MCB 1 4 20 2 4 20 3 4 20 4 5 20 5 6 26 6 7 17 7 8 27 8 9 23 8 10 23 8 11 27 11 12 17 12 13 26 13 14 17 13 32 26 14 15 9 15 16 4 15 17 22 17 18 26 18 19 26 19 20 26 20 21 26 21 22 26 22 23 26 23 24 26 24 25 26 25 26 26 26 27 26 27 28 26 28 29 26 29 30 26 30 31 26 32 33 17 33 34 9 34 35 4 34 36 22 36 37 26 37 38 26 38 39 26 39 40 26 40 41 26 41 42 26 42 43 26 43 44 26 44 45 26 45 46 26 46 47 26 47 48 26 48 49 26 49 50 26 # bond angles # NBA 57 # IB JB KB MCB 1 4 2 12 1 4 3 12 1 4 5 12 2 4 3 12 2 4 5 12 3 4 5 12 4 5 6 14 5 6 7 14 6 7 8 25 7 8 9 13 7 8 10 13 7 8 11 4 9 8 10 28 9 8 11 13 10 8 11 13 8 11 12 25 11 12 13 14 12 13 14 12 12 13 32 12 14 13 32 12 13 14 15 21 14 15 16 30 14 15 17 15 16 15 17 34 15 17 18 14 17 18 19 14 18 19 20 14 19 20 21 14 20 21 22 14 21 22 23 14 22 23 24 14 23 24 25 14 24 25 26 14 25 26 27 14 26 27 28 14 27 28 29 14 28 29 30 14 29 30 31 14 13 32 33 14 32 33 34 21 33 34 35 30 33 34 36 15 35 34 36 34 34 36 37 14 36 37 38 14 37 38 39 14 38 39 40 14 39 40 41 14 40 41 42 14 41 42 43 14 42 43 44 14 43 44 45 14 44 45 46 14 45 46 47 14 46 47 48 14 47 48 49 14 48 49 50 14 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 14 12 32 13 2 15 14 17 16 1 34 33 36 35 1 # dihedrals # NDA 43 # IB JB KB LB MCB 1 4 5 6 14 4 5 6 7 27 4 5 6 7 28 5 6 7 8 14 6 7 8 11 24 6 7 8 11 25 7 8 11 12 24 7 8 11 12 25 8 11 12 13 14 11 12 13 32 17 12 13 14 15 14 12 13 32 33 17 13 14 15 17 29 14 15 17 18 20 15 17 18 19 17 17 18 19 20 17 18 19 20 21 17 19 20 21 22 17 20 21 22 23 17 21 22 23 24 17 22 23 24 25 17 23 24 25 26 17 24 25 26 27 17 25 26 27 28 17 26 27 28 29 17 27 28 29 30 17 28 29 30 31 17 13 32 33 34 14 32 33 34 36 29 33 34 36 37 20 34 36 37 38 17 36 37 38 39 17 37 38 39 40 17 38 39 40 41 17 39 40 41 42 17 40 41 42 43 17 41 42 43 44 17 42 43 44 45 17 43 44 45 46 17 44 45 46 47 17 45 46 47 48 17 46 47 48 49 17 47 48 49 50 17 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 0.54000 0 4 2 3 4 5 2 IO1 2 16 -0.63500 0 3 3 4 5 3 IO2 2 16 -0.63500 0 2 4 5 4 IO3 2 16 -0.63500 0 1 5 5 IO4 2 16 -0.63500 1 0 # 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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb45a4.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 END MTBUILDBLSOLVENT #@BLOCKTYPE mtb45a4.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 mtb45a4.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 mtb45a4.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 mtb45a4.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 mtb45a4.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 mtb45a4.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 MTBUILDBLEND #@BLOCKTYPE mtb45a4.dat INI TYPE NH3+ # building block (residue, nucleotide, etc.) # RNME NH3+ # number of atoms, number of atoms to be replaced # NMAT NREP 5 3 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H1 18 1 0.24800 0 4 2 3 4 5 2 H2 18 1 0.24800 0 3 3 4 5 #replacing atoms 3 N 7 14 0.12900 0 4 H3 18 1 0.24800 0 5 CA 12 3 0.12700 1 # bonds # NB 2 # IB JB MCB 1 3 2 2 3 2 # bond angles # NBA 6 # IB JB KB MCB 1 3 2 9 1 3 4 9 1 3 5 10 2 3 4 9 2 3 5 10 4 3 5 10 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 2 3 5 6 14 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE mtb45a4.dat INI TYPE NH2 # building block (residue, nucleotide, etc.) # RNME NH2 # number of atoms, number of atoms to be replaced # NMAT NREP 3 2 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H1 18 1 0.41500 0 3 2 3 4 #replacing atoms 2 N 6 14 -0.83000 0 3 H2 18 1 0.41500 1 # bonds # NB 1 # IB JB MCB 1 2 2 # bond angles # NBA 3 # IB JB KB MCB 1 2 3 9 1 2 4 10 3 2 4 10 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 1 2 4 5 14 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE mtb45a4.dat INI TYPE NPRO # building block (residue, nucleotide, etc.) # RNME NPRO # number of atoms, number of atoms to be replaced # NMAT NREP 7 5 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H1 18 1 0.24800 0 4 2 3 4 7 2 H2 18 1 0.24800 0 3 3 4 7 #replacing atoms 3 N 7 14 0.12800 0 4 CA 12 3 0.18800 0 5 CB 13 4 0.00000 0 6 CG 13 4 0.00000 0 7 CD 13 4 0.18800 1 # bonds # NB 7 # IB JB MCB 1 3 2 2 3 2 3 4 20 3 7 20 4 5 26 5 6 26 6 7 26 # bond angles # NBA 10 # IB JB KB MCB 1 3 2 9 1 3 4 10 1 3 7 10 2 3 4 10 2 3 7 10 4 3 7 20 3 4 5 12 4 5 6 12 5 6 7 12 3 7 6 12 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 2 3 4 8 14 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE mtb45a4.dat TER TYPE COO- # building block (residue, nucleotide, etc.) # RNME COO- # number of atoms, number of preceding exclusions # NMAT NREP 3 -2 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C 11 12 0.27000 0 2 2 3 2 O1 2 16 -0.63500 0 1 3 3 O2 2 16 -0.63500 1 0 # bonds # NB 2 # IB JB MCB 1 2 5 1 3 5 # bond angles # NBA 3 # IB JB KB MCB 0 1 2 21 0 1 3 21 2 1 3 37 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE END MTBUILDBLEND #@BLOCKTYPE mtb45a4.dat TER TYPE COOH # building block (residue, nucleotide, etc.) # RNME COOH # number of atoms, number of preceding exclusions # NMAT NREP 4 -2 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C 11 12 0.53000 0 3 2 3 4 2 O1 1 16 -0.38000 0 1 3 3 O2 3 16 -0.54800 0 1 4 4 H 18 1 0.39800 1 0 # bonds # NB 3 # IB JB MCB 1 2 4 1 3 12 3 4 1 # bond angles # NBA 1 # IB JB KB MCB 1 3 4 11 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 0 1 3 4 3 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE mtb45a4.dat INI TYPE D5OH # building block (residue, nucleotide, etc.) # RNME D5OH # number of atoms, number of atoms to be replaced # NMAT NREP 5 5 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H5* 18 1 0.398 0 2 O1P -1 1 0.0 0 3 O2P -1 1 0.0 0 4 O5* 3 16 -0.548 0 5 C5* 13 4 0.150 1 # bonds # NB 2 # IB JB MCB 1 4 1 4 5 19 # bond angles # NBA 1 # IB JB KB MCB 1 4 5 11 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 1 4 5 6 12 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE mtb45a4.dat INI TYPE 5OH # building block (residue, nucleotide, etc.) # RNME 5OH # number of atoms, number of atoms to be replaced # NMAT NREP 5 5 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H5* 18 1 0.398 0 2 O1P -1 1 0.0 0 3 O2P -1 1 0.0 0 4 O5* 3 16 -0.548 0 5 C5* 13 4 0.150 1 # bonds # NB 2 # IB JB MCB 1 4 1 4 5 19 # bond angles # NBA 1 # IB JB KB MCB 1 4 5 11 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 1 4 5 6 12 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE mtb45a4.dat TER TYPE D3OH # building block (residue, nucleotide, etc.) # RNME D3OH # number of atoms, number of preceding exclusions # NMAT NREP 4 -3 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C2* 44 4 0.00000 1 2 2 3 2 C3* 12 3 0.15000 0 2 3 4 3 O3* 3 16 -0.54800 0 1 4 4 H3* 18 1 0.39800 1 0 # bonds # NB 2 # IB JB MCB 2 3 19 3 4 1 # bond angles # NBA 1 # IB JB KB MCB 2 3 4 11 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 0 2 3 4 12 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE mtb45a4.dat TER TYPE 3OH # building block (residue, nucleotide, etc.) # RNME 3OH # number of atoms, number of preceding exclusions # NMAT NREP 6 -5 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C2* 12 3 0.15 0 4 2 3 4 5 2 O2* 3 16 -0.548 0 2 3 4 3 H2* 18 1 0.398 1 0 4 C3* 12 3 0.15000 0 2 5 6 5 O3* 3 16 -0.54800 0 1 6 6 H3* 18 1 0.39800 1 0 # bonds # NB 5 # IB JB MCB 1 2 19 1 4 25 2 3 1 4 5 19 5 6 1 # bond angles # NBA 4 # IB JB KB MCB 1 2 3 11 2 1 4 8 1 4 5 8 4 5 6 11 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 0 4 5 6 14 #@FREELINE END