TITLE File : mtb53a6.dat Force field : 53A6 (condensed-phase simulations) Reference : Oostenbrink et al. J. Comput. Chem. 2004, 25, 1656-1676 File content : molecular topology building blocks (alpha amino acids, nucleic acids, lipids) Format : GROMOS96 Initial file : WFVG, CO, Zuerich, March 2004 Time stamp : PHH, Thu Nov 10 21:52:57 CET 2011 Remark : Change from 53A(B)5 involves different charges for the polar amino-acid sidechains Remark : Parameterization against hydration properties of model compounds Remark : This file only differs from the corresponding file in 53A(B)5 in the charges of polar amino-acid sidechains Remark : DG, NS, Oct 07: exclusion errors corrected in FMNR, ATP, TMP, THF and HEME Remark : DG, CO, Jan 08: errors in improper dihedrals 21-24 in NADH corrected Remark : The above changes are propagated to subsequent force-field versions Remark : PHH, May 2011 - 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 53A6 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 mtb53a6.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 6 14 -0.31000 0 4 2 3 4 5 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 4 4 5 6 7 4 CB 16 5 0.00000 1 1 5 # trailing atoms #ATOM ANM IACM MASS CGMICGM 5 C 12 12 0.45000 0 6 O 1 16 -0.45000 1 # bonds # NB 6 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 5 27 5 6 5 5 7 10 # bond angles # NBA 9 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 5 13 4 3 5 13 3 5 6 30 3 5 7 19 6 5 7 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 5 4 2 5 3 7 6 1 # dihedrals # NDA 3 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 5 39 1 3 5 7 40 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 16 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 16 17 18 4 CB 15 4 0.00000 0 3 5 6 16 5 CG 15 4 0.00000 1 2 6 7 6 CD 15 4 0.09000 0 3 7 8 9 7 NE 11 14 -0.11000 0 4 8 9 10 13 8 HE 21 1 0.24000 0 1 9 9 CZ 12 12 0.34000 0 6 10 11 12 13 14 15 10 NH1 10 14 -0.26000 0 3 11 12 13 11 HH11 21 1 0.24000 0 1 12 12 HH12 21 1 0.24000 0 0 13 NH2 10 14 -0.26000 0 2 14 15 14 HH21 21 1 0.24000 0 1 15 15 HH22 21 1 0.24000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 16 C 12 12 0.45000 0 17 O 1 16 -0.45000 1 # bonds # NB 17 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 16 27 4 5 27 5 6 27 6 7 21 7 8 2 7 9 11 9 10 11 9 13 11 10 11 2 10 12 2 13 14 2 13 15 2 16 17 5 16 18 10 # bond angles # NBA 24 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 16 13 4 3 16 13 3 4 5 15 4 5 6 15 5 6 7 13 6 7 8 20 6 7 9 33 8 7 9 23 7 9 10 28 7 9 13 28 10 9 13 28 9 10 11 23 9 10 12 23 11 10 12 24 9 13 14 23 9 13 15 23 14 13 15 24 3 16 17 30 3 16 18 19 17 16 18 33 # improper dihedrals # NIDA 7 # IB JB KB LB MCB 1 -1 3 2 1 3 1 16 4 2 7 6 9 8 1 9 10 13 7 1 10 11 12 9 1 13 14 15 9 1 16 3 18 17 1 # dihedrals # NDA 10 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 16 39 1 3 4 5 34 1 3 16 18 40 3 4 5 6 34 4 5 6 7 34 5 6 7 9 39 6 7 9 10 14 7 9 10 11 14 7 9 13 14 14 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 15 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 15 16 17 4 CB 15 4 0.00000 1 3 5 6 15 5 CG 15 4 0.00000 0 2 6 7 6 CD 15 4 0.00000 1 3 7 8 9 7 NE 11 14 -0.31000 0 4 8 9 10 12 8 HE 21 1 0.31000 1 1 9 9 CZ 12 12 0.26600 0 5 10 11 12 13 14 10 NH1 11 14 -0.67400 0 2 11 12 11 HH1 21 1 0.40800 1 0 12 NH2 10 14 -0.88000 0 2 13 14 13 HH21 21 1 0.44000 0 1 14 14 HH22 21 1 0.44000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 15 C 12 12 0.45000 0 16 O 1 16 -0.45000 1 # bonds # NB 16 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 15 27 4 5 27 5 6 27 6 7 21 7 8 2 7 9 11 9 10 11 9 12 11 10 11 2 12 13 2 12 14 2 15 16 5 15 17 10 # bond angles # NBA 22 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 15 13 4 3 15 13 3 4 5 15 4 5 6 15 5 6 7 13 6 7 8 20 6 7 9 33 8 7 9 23 7 9 10 28 7 9 12 28 10 9 12 28 9 10 11 23 9 12 13 23 9 12 14 23 13 12 14 24 3 15 16 30 3 15 17 19 16 15 17 33 # improper dihedrals # NIDA 6 # IB JB KB LB MCB 1 -1 3 2 1 3 1 15 4 2 7 6 9 8 1 9 10 12 7 1 12 13 14 9 1 15 3 17 16 1 # dihedrals # NDA 10 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 15 39 1 3 4 5 34 1 3 15 17 40 3 4 5 6 34 4 5 6 7 34 5 6 7 9 39 6 7 9 10 14 7 9 10 11 14 7 9 12 13 14 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 10 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 10 11 12 4 CB 15 4 0.00000 1 4 5 6 7 10 5 CG 12 12 0.29000 0 4 6 7 8 9 6 OD1 1 16 -0.45000 0 1 7 7 ND2 7 14 -0.72000 0 2 8 9 8 HD21 21 1 0.44000 0 1 9 9 HD22 21 1 0.44000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 10 C 12 12 0.45000 0 11 O 1 16 -0.45000 1 # bonds # NB 11 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 10 27 4 5 27 5 6 5 5 7 9 7 8 2 7 9 2 10 11 5 10 12 10 # bond angles # NBA 16 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 10 13 4 3 10 13 3 4 5 15 4 5 6 30 4 5 7 19 6 5 7 33 5 7 8 23 5 7 9 23 8 7 9 24 3 10 11 30 3 10 12 19 11 10 12 33 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 1 -1 3 2 1 3 1 10 4 2 5 6 7 4 1 7 8 9 5 1 10 3 12 11 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 10 39 1 3 4 5 34 1 3 10 12 40 3 4 5 7 40 4 5 7 8 14 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 10 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 10 11 12 4 CB 15 4 0.00000 1 4 5 6 7 10 5 CG 12 12 0.29000 0 4 6 7 8 9 6 OD1 1 16 -0.45000 0 1 7 7 ND2 8 14 -0.72000 0 2 8 9 8 HD21 21 1 0.44000 0 1 9 9 HD22 21 1 0.44000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 10 C 12 12 0.45000 0 11 O 1 16 -0.45000 1 # bonds # NB 11 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 10 27 4 5 27 5 6 5 5 7 9 7 8 2 7 9 2 10 11 5 10 12 10 # bond angles # NBA 16 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 10 13 4 3 10 13 3 4 5 15 4 5 6 30 4 5 7 19 6 5 7 33 5 7 8 23 5 7 9 23 8 7 9 24 3 10 11 30 3 10 12 19 11 10 12 33 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 1 -1 3 2 1 3 1 10 4 2 5 6 7 4 1 7 8 9 5 1 10 3 12 11 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 10 39 1 3 4 5 34 1 3 10 12 40 3 4 5 7 40 4 5 7 8 14 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 8 9 10 4 CB 15 4 0.00000 1 4 5 6 7 8 5 CG 12 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 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 27 5 6 6 5 7 6 8 9 5 8 10 10 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 15 4 5 6 22 4 5 7 22 6 5 7 38 3 8 9 30 3 8 10 19 9 8 10 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 8 4 2 5 6 7 4 1 8 3 10 9 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 39 1 3 4 5 34 1 3 8 10 40 3 4 5 6 40 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 9 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 9 10 11 4 CB 15 4 0.00000 1 4 5 6 7 9 5 CG 12 12 0.33000 0 3 6 7 8 6 OD1 1 16 -0.45000 0 1 7 7 OD2 3 16 -0.28800 0 1 8 8 HD2 21 1 0.40800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 9 C 12 12 0.45000 0 10 O 1 16 -0.45000 1 # bonds # NB 10 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 9 27 4 5 27 5 6 5 5 7 13 7 8 1 9 10 5 9 11 10 # bond angles # NBA 14 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 9 13 4 3 9 13 3 4 5 15 4 5 6 30 4 5 7 19 6 5 7 33 5 7 8 12 3 9 10 30 3 9 11 19 10 9 11 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 9 4 2 5 6 7 4 1 9 3 11 10 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 9 39 1 3 4 5 34 1 3 9 11 40 3 4 5 7 40 4 5 7 8 12 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 6 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 1 5 4 5 6 7 8 4 CB 15 4 -0.10000 0 2 5 6 5 SG 23 32 -0.40000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 12 12 0.45000 0 7 O 1 16 -0.45000 1 # bonds # NB 7 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 6 27 4 5 32 6 7 5 6 8 10 # bond angles # NBA 10 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 6 13 4 3 6 13 3 4 5 16 3 6 7 30 3 6 8 19 7 6 8 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 6 4 2 6 3 8 7 1 # dihedrals # NDA 4 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 6 39 1 3 4 5 34 1 3 6 8 40 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 7 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 1 5 4 5 7 8 9 4 CB 15 4 0.15000 0 3 5 6 7 5 SG 23 32 -0.37000 0 1 6 6 HG 21 1 0.22000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 7 C 12 12 0.45000 0 8 O 1 16 -0.45000 1 # bonds # NB 8 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 7 27 4 5 32 5 6 8 7 8 5 7 9 10 # bond angles # NBA 11 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 7 13 4 3 7 13 3 4 5 16 4 5 6 3 3 7 8 30 3 7 9 19 8 7 9 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 7 4 2 7 3 9 8 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 39 1 3 4 5 34 1 3 7 9 40 3 4 5 6 26 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 6 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 6 7 8 4 CB 15 4 0.00000 0 3 -5 5 6 5 SG 23 32 0.00000 1 2 -5 -4 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 12 12 0.45000 0 7 O 1 16 -0.45000 1 # bonds # NB 8 # IB JB MCB -5 5 36 1 2 2 1 3 21 3 4 27 3 6 27 4 5 32 6 7 5 6 8 10 # bond angles # NBA 12 # IB JB KB MCB -4 -5 5 6 -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 6 13 4 3 6 13 3 4 5 16 -5 5 4 6 3 6 7 30 3 6 8 19 7 6 8 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 6 4 2 6 3 8 7 1 # dihedrals # NDA 7 # IB JB KB LB MCB 5 -5 -4 -3 26 -4 -5 5 4 21 -2 -1 1 3 14 -1 1 3 6 39 1 3 4 5 34 1 3 6 8 40 3 4 5 -5 26 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 6 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 6 7 8 4 CB 15 4 0.00000 0 2 5 6 5 SG 23 32 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 12 12 0.45000 0 7 O 1 16 -0.45000 1 # bonds # NB 7 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 6 27 4 5 32 6 7 5 6 8 10 # bond angles # NBA 10 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 6 13 4 3 6 13 3 4 5 16 3 6 7 30 3 6 8 19 7 6 8 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 6 4 2 6 3 8 7 1 # dihedrals # NDA 4 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 6 39 1 3 4 5 34 1 3 6 8 40 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 11 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 11 12 13 4 CB 15 4 0.00000 0 3 5 6 11 5 CG 15 4 0.00000 1 3 6 7 8 6 CD 12 12 0.29000 0 4 7 8 9 10 7 OE1 1 16 -0.45000 0 1 8 8 NE2 7 14 -0.72000 0 2 9 10 9 HE21 21 1 0.44000 0 1 10 10 HE22 21 1 0.44000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 11 C 12 12 0.45000 0 12 O 1 16 -0.45000 1 # bonds # NB 12 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 11 27 4 5 27 5 6 27 6 7 5 6 8 9 8 9 2 8 10 2 11 12 5 11 13 10 # bond angles # NBA 17 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 11 13 4 3 11 13 3 4 5 15 4 5 6 15 5 6 7 30 5 6 8 19 7 6 8 33 6 8 9 23 6 8 10 23 9 8 10 24 3 11 12 30 3 11 13 19 12 11 13 33 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 1 -1 3 2 1 3 1 11 4 2 6 7 8 5 1 8 9 10 6 1 11 3 13 12 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 11 39 1 3 4 5 34 1 3 11 13 40 3 4 5 6 34 4 5 6 8 40 5 6 8 9 14 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 9 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 9 10 11 4 CB 15 4 0.00000 0 3 5 6 9 5 CG 15 4 0.00000 1 3 6 7 8 6 CD 12 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 12 12 0.45000 0 10 O 1 16 -0.45000 1 # bonds # NB 10 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 9 27 4 5 27 5 6 27 6 7 6 6 8 6 9 10 5 9 11 10 # bond angles # NBA 14 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 9 13 4 3 9 13 3 4 5 15 4 5 6 15 5 6 7 22 5 6 8 22 7 6 8 38 3 9 10 30 3 9 11 19 10 9 11 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 9 4 2 6 7 8 5 1 9 3 11 10 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 9 39 1 3 4 5 34 1 3 9 11 40 3 4 5 6 34 4 5 6 8 40 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 10 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 10 11 12 4 CB 15 4 0.00000 0 3 5 6 10 5 CG 15 4 0.00000 1 3 6 7 8 6 CD 12 12 0.33000 0 3 7 8 9 7 OE1 1 16 -0.45000 0 1 8 8 OE2 3 16 -0.28800 0 1 9 9 HE2 21 1 0.40800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 10 C 12 12 0.45000 0 11 O 1 16 -0.45000 1 # bonds # NB 11 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 10 27 4 5 27 5 6 27 6 7 5 6 8 13 8 9 1 10 11 5 10 12 10 # bond angles # NBA 15 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 10 13 4 3 10 13 3 4 5 15 4 5 6 15 5 6 7 30 5 6 8 19 7 6 8 33 6 8 9 12 3 10 11 30 3 10 12 19 11 10 12 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 10 4 2 6 7 8 5 1 10 3 12 11 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 10 39 1 3 4 5 34 1 3 10 12 40 3 4 5 6 34 4 5 6 8 40 5 6 8 9 12 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 3 2 3 4 2 H 21 1 0.31000 1 1 3 3 CA 15 4 0.00000 1 3 4 5 6 # trailing atoms #ATOM ANM IACM MASS CGMICGM 4 C 12 12 0.45000 0 5 O 1 16 -0.45000 1 # bonds # NB 5 # IB JB MCB 1 2 2 1 3 21 3 4 27 4 5 5 4 6 10 # bond angles # NBA 7 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 3 4 5 30 3 4 6 19 5 4 6 33 # improper dihedrals # NIDA 2 # IB JB KB LB MCB 1 -1 3 2 1 4 3 6 5 1 # dihedrals # NDA 3 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 4 39 1 3 4 6 40 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE HISA # building block (residue, nucleotide, etc.) # RNME HISA # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 13 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 13 14 15 4 CB 15 4 0.00000 1 8 5 6 7 8 9 10 12 13 5 CG 12 12 0.00000 0 7 6 7 8 9 10 11 12 6 ND1 9 14 -0.05000 0 6 7 8 9 10 11 12 7 HD1 21 1 0.31000 0 4 8 10 11 12 8 CD2 12 12 0.00000 0 4 9 10 11 12 9 HD2 20 1 0.14000 0 2 10 12 10 CE1 12 12 0.00000 0 2 11 12 11 HE1 20 1 0.14000 0 1 12 12 NE2 9 14 -0.54000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 13 C 12 12 0.45000 0 14 O 1 16 -0.45000 1 # bonds # NB 15 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 13 27 4 5 27 5 6 10 5 8 10 6 7 2 6 10 10 8 9 3 8 12 10 10 11 3 10 12 10 13 14 5 13 15 10 # bond angles # NBA 23 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 13 13 4 3 13 13 3 4 5 15 4 5 6 37 4 5 8 37 6 5 8 7 5 6 7 36 5 6 10 7 7 6 10 36 5 8 9 36 5 8 12 7 9 8 12 36 6 10 11 36 6 10 12 7 11 10 12 36 8 12 10 7 3 13 14 30 3 13 15 19 14 13 15 33 # improper dihedrals # NIDA 12 # IB JB KB LB MCB 1 -1 3 2 1 3 1 13 4 2 5 6 8 4 1 5 6 10 12 1 5 8 12 10 1 6 5 8 12 1 6 5 10 7 1 6 10 12 8 1 8 5 6 10 1 8 5 12 9 1 10 6 12 11 1 13 3 15 14 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 13 39 1 3 4 5 34 1 3 13 15 40 3 4 5 6 40 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE HISB # building block (residue, nucleotide, etc.) # RNME HISB # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 13 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 13 14 15 4 CB 15 4 0.00000 1 7 5 6 7 8 9 11 13 5 CG 12 12 0.00000 0 7 6 7 8 9 10 11 12 6 ND1 9 14 -0.54000 0 6 7 8 9 10 11 12 7 CD2 12 12 0.00000 0 5 8 9 10 11 12 8 HD2 20 1 0.14000 0 3 9 11 12 9 CE1 12 12 0.00000 0 3 10 11 12 10 HE1 20 1 0.14000 0 2 11 12 11 NE2 9 14 -0.05000 0 1 12 12 HE2 21 1 0.31000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 13 C 12 12 0.45000 0 14 O 1 16 -0.45000 1 # bonds # NB 15 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 13 27 4 5 27 5 6 10 5 7 10 6 9 10 7 8 3 7 11 10 9 10 3 9 11 10 11 12 2 13 14 5 13 15 10 # bond angles # NBA 23 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 13 13 4 3 13 13 3 4 5 15 4 5 6 37 4 5 7 37 6 5 7 7 5 6 9 7 5 7 8 36 5 7 11 7 8 7 11 36 6 9 10 36 6 9 11 7 10 9 11 36 7 11 9 7 7 11 12 36 9 11 12 36 3 13 14 30 3 13 15 19 14 13 15 33 # improper dihedrals # NIDA 12 # IB JB KB LB MCB 1 -1 3 2 1 3 1 13 4 2 5 6 7 4 1 5 6 9 11 1 5 7 11 9 1 6 5 7 11 1 6 9 11 7 1 7 5 6 9 1 7 5 11 8 1 9 6 11 10 1 11 7 9 12 1 13 3 15 14 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 13 39 1 3 4 5 34 1 3 13 15 40 3 4 5 6 40 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE HISH # building block (residue, nucleotide, etc.) # RNME HISH # number of atoms, number of preceding exclusions # NMAT NLIN 15 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 14 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 14 15 16 4 CB 15 4 0.00000 1 8 5 6 7 8 9 10 12 14 5 CG 12 12 -0.05000 0 8 6 7 8 9 10 11 12 13 6 ND1 9 14 0.38000 0 7 7 8 9 10 11 12 13 7 HD1 21 1 0.30000 0 4 8 10 11 12 8 CD2 12 12 -0.10000 0 5 9 10 11 12 13 9 HD2 20 1 0.10000 0 3 10 12 13 10 CE1 12 12 -0.34000 0 3 11 12 13 11 HE1 20 1 0.10000 0 2 12 13 12 NE2 9 14 0.31000 0 1 13 13 HE2 21 1 0.30000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 14 C 12 12 0.45000 0 15 O 1 16 -0.45000 1 # bonds # NB 16 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 14 27 4 5 27 5 6 10 5 8 10 6 7 2 6 10 10 8 9 3 8 12 10 10 11 3 10 12 10 12 13 2 14 15 5 14 16 10 # bond angles # NBA 25 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 14 13 4 3 14 13 3 4 5 15 4 5 6 37 4 5 8 37 6 5 8 7 5 6 7 36 5 6 10 7 7 6 10 36 5 8 9 36 5 8 12 7 9 8 12 36 6 10 11 36 6 10 12 7 11 10 12 36 8 12 10 7 8 12 13 36 10 12 13 36 3 14 15 30 3 14 16 19 15 14 16 33 # improper dihedrals # NIDA 13 # IB JB KB LB MCB 1 -1 3 2 1 3 1 14 4 2 5 6 8 4 1 5 6 10 12 1 5 8 12 10 1 6 5 8 12 1 6 5 10 7 1 6 10 12 8 1 8 5 6 10 1 8 5 12 9 1 10 6 12 11 1 12 8 10 13 1 14 3 16 15 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 14 39 1 3 4 5 34 1 3 14 16 40 3 4 5 6 40 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE HIS1 # building block (residue, nucleotide, etc.) # RNME HIS1 # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 13 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 13 14 15 4 CB 15 4 0.00000 1 8 5 6 7 8 9 10 12 13 5 CG 12 12 0.00000 0 8 -1 6 7 8 9 10 11 12 6 ND1 9 14 -0.05000 0 7 -1 7 8 9 10 11 12 7 HD1 21 1 0.31000 0 4 8 10 11 12 8 CD2 12 12 0.00000 0 5 -1 9 10 11 12 9 HD2 20 1 0.14000 0 3 -1 10 12 10 CE1 12 12 0.00000 0 3 -1 11 12 11 HE1 20 1 0.14000 0 2 -1 12 12 NE2 9 14 -0.54000 1 5 -5 -4 -3 -2 -1 # trailing atoms #ATOM ANM IACM MASS CGMICGM 13 C 12 12 0.45000 0 14 O 1 16 -0.45000 1 # bonds # NB 16 # IB JB MCB -1 12 37 1 2 2 1 3 21 3 4 27 3 13 27 4 5 27 5 6 10 5 8 10 6 7 2 6 10 10 8 9 3 8 12 10 10 11 3 10 12 10 13 14 5 13 15 10 # bond angles # NBA 29 # IB JB KB MCB -5 -1 12 2 -4 -1 12 2 -3 -1 12 2 -2 -1 12 2 -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 13 13 4 3 13 13 3 4 5 15 4 5 6 37 4 5 8 37 6 5 8 7 5 6 7 36 5 6 10 7 7 6 10 36 5 8 9 36 5 8 12 7 9 8 12 36 6 10 11 36 6 10 12 7 11 10 12 36 -1 12 8 34 -1 12 10 34 8 12 10 7 3 13 14 30 3 13 15 19 14 13 15 33 # improper dihedrals # NIDA 12 # IB JB KB LB MCB 1 -1 3 2 1 3 1 13 4 2 5 6 8 4 1 5 6 10 12 1 5 8 12 10 1 6 5 8 12 1 6 5 10 7 1 6 10 12 8 1 8 5 6 10 1 8 5 12 9 1 10 6 12 11 1 13 3 15 14 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -2 -1 12 8 38 -1 1 3 13 39 1 3 4 5 34 1 3 13 15 40 3 4 5 6 40 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE HIS2 # building block (residue, nucleotide, etc.) # RNME HIS2 # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 4 2 3 4 13 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 13 14 15 4 CB 15 4 0.00000 1 8 5 6 7 8 9 10 12 13 5 CG 12 12 0.00000 0 8 -1 6 7 8 9 10 11 12 6 ND1 9 14 -0.05000 0 7 -1 7 8 9 10 11 12 7 HD1 21 1 0.31000 0 4 8 10 11 12 8 CD2 12 12 0.00000 0 5 -1 9 10 11 12 9 HD2 20 1 0.14000 0 3 -1 10 12 10 CE1 12 12 0.00000 0 3 -1 11 12 11 HE1 20 1 0.14000 0 2 -1 12 12 NE2 9 14 -0.54000 1 6 -48 -5 -4 -3 -2 -1 # trailing atoms #ATOM ANM IACM MASS CGMICGM 13 C 12 12 0.45000 0 14 O 1 16 -0.45000 1 # bonds # NB 16 # IB JB MCB -1 12 37 1 2 2 1 3 21 3 4 27 3 13 27 4 5 27 5 6 10 5 8 10 6 7 2 6 10 10 8 9 3 8 12 10 10 11 3 10 12 10 13 14 5 13 15 10 # bond angles # NBA 29 # IB JB KB MCB -5 -1 12 2 -4 -1 12 2 -3 -1 12 2 -2 -1 12 2 -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 13 13 4 3 13 13 3 4 5 15 4 5 6 37 4 5 8 37 6 5 8 7 5 6 7 36 5 6 10 7 7 6 10 36 5 8 9 36 5 8 12 7 9 8 12 36 6 10 11 36 6 10 12 7 11 10 12 36 -1 12 8 34 -1 12 10 34 8 12 10 7 3 13 14 30 3 13 15 19 14 13 15 33 # improper dihedrals # NIDA 12 # IB JB KB LB MCB 1 -1 3 2 1 3 1 13 4 2 5 6 8 4 1 5 6 10 12 1 5 8 12 10 1 6 5 8 12 1 6 5 10 7 1 6 10 12 8 1 8 5 6 10 1 8 5 12 9 1 10 6 12 11 1 13 3 15 14 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -2 -1 12 8 38 -1 1 3 13 39 1 3 4 5 34 1 3 13 15 40 3 4 5 6 40 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 0.00000 1 5 2 3 4 7 8 2 CA 14 3 0.00000 0 6 3 4 7 8 9 10 3 CB 18 4 0.00000 1 4 4 5 7 8 4 CG 14 3 0.26600 0 3 5 6 7 5 OD1 3 16 -0.67400 0 2 6 7 6 HD1 21 1 0.40800 1 0 7 CD2 18 4 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 10 # IB JB MCB 1 2 21 1 7 21 2 3 27 2 8 27 3 4 27 4 5 18 4 7 27 5 6 1 8 9 5 8 10 10 # bond angles # NBA 15 # IB JB KB MCB -1 1 2 31 -1 1 7 31 2 1 7 21 1 2 3 13 1 2 8 13 3 2 8 13 2 3 4 13 3 4 5 13 3 4 7 13 5 4 7 13 4 5 6 12 1 7 4 13 2 8 9 30 2 8 10 19 9 8 10 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 2 7 1 2 1 8 3 2 5 3 7 4 2 8 2 10 9 1 # dihedrals # NDA 8 # IB JB KB LB MCB -2 -1 1 2 14 -1 1 2 8 39 2 1 7 4 39 1 2 3 4 34 1 2 8 10 40 2 3 4 7 34 3 4 5 6 23 3 4 7 1 34 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 1 6 4 5 6 8 9 10 4 CB 14 3 0.00000 0 4 5 6 7 8 5 CG1 15 4 0.00000 0 2 6 7 6 CG2 16 5 0.00000 0 0 7 CD 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 27 4 6 27 5 7 27 8 9 5 8 10 10 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 15 3 4 6 15 5 4 6 15 4 5 7 15 3 8 9 30 3 8 10 19 9 8 10 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 8 4 2 4 5 6 3 2 8 3 10 9 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 39 1 3 4 5 34 1 3 8 10 40 3 4 5 7 34 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 8 9 10 4 CB 15 4 0.00000 1 4 5 6 7 8 5 CG 14 3 0.00000 0 2 6 7 6 CD1 16 5 0.00000 0 1 7 7 CD2 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 27 5 6 27 5 7 27 8 9 5 8 10 10 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 15 4 5 6 15 4 5 7 15 6 5 7 15 3 8 9 30 3 8 10 19 9 8 10 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 8 4 2 4 6 7 5 2 8 3 10 9 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 39 1 3 4 5 34 1 3 8 10 40 3 4 5 6 34 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 11 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 11 12 13 4 CB 15 4 0.00000 1 3 5 6 11 5 CG 15 4 0.00000 0 2 6 7 6 CD 15 4 0.00000 1 2 7 8 7 CE 15 4 -0.24000 0 3 8 9 10 8 NZ 7 14 -0.64000 0 2 9 10 9 HZ1 21 1 0.44000 0 1 10 10 HZ2 21 1 0.44000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 11 C 12 12 0.45000 0 12 O 1 16 -0.45000 1 # bonds # NB 12 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 11 27 4 5 27 5 6 27 6 7 27 7 8 21 8 9 2 8 10 2 11 12 5 11 13 10 # bond angles # NBA 16 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 11 13 4 3 11 13 3 4 5 15 4 5 6 15 5 6 7 15 6 7 8 15 7 8 9 11 7 8 10 11 9 8 10 10 3 11 12 30 3 11 13 19 12 11 13 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 11 4 2 11 3 13 12 1 # dihedrals # NDA 8 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 11 39 1 3 4 5 34 1 3 11 13 40 3 4 5 6 34 4 5 6 7 34 5 6 7 8 34 6 7 8 9 29 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 12 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 12 13 14 4 CB 15 4 0.00000 1 3 5 6 12 5 CG 15 4 0.00000 0 2 6 7 6 CD 15 4 0.00000 1 2 7 8 7 CE 15 4 0.12700 0 4 8 9 10 11 8 NZ 8 14 0.12900 0 3 9 10 11 9 HZ1 21 1 0.24800 0 2 10 11 10 HZ2 21 1 0.24800 0 1 11 11 HZ3 21 1 0.24800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 12 C 12 12 0.45000 0 13 O 1 16 -0.45000 1 # bonds # NB 13 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 12 27 4 5 27 5 6 27 6 7 27 7 8 21 8 9 2 8 10 2 8 11 2 12 13 5 12 14 10 # bond angles # NBA 19 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 12 13 4 3 12 13 3 4 5 15 4 5 6 15 5 6 7 15 6 7 8 15 7 8 9 11 7 8 10 11 7 8 11 11 9 8 10 10 9 8 11 10 10 8 11 10 3 12 13 30 3 12 14 19 13 12 14 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 12 4 2 12 3 14 13 1 # dihedrals # NDA 8 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 12 39 1 3 4 5 34 1 3 12 14 40 3 4 5 6 34 4 5 6 7 34 5 6 7 8 34 6 7 8 9 29 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 8 9 10 4 CB 15 4 0.00000 1 3 5 6 8 5 CG 15 4 0.24100 0 2 6 7 6 SD 23 32 -0.48200 0 1 7 7 CE 16 5 0.24100 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 27 5 6 32 6 7 31 8 9 5 8 10 10 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 15 4 5 6 16 5 6 7 4 3 8 9 30 3 8 10 19 9 8 10 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 8 4 2 8 3 10 9 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 39 1 3 4 5 34 1 3 8 10 40 3 4 5 6 34 4 5 6 7 26 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 16 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 16 17 18 4 CB 15 4 0.00000 0 8 5 6 7 8 9 10 12 16 5 CG 12 12 0.00000 1 9 6 7 8 9 10 11 12 13 14 6 CD1 12 12 -0.14000 0 8 7 8 9 10 11 12 14 15 7 HD1 20 1 0.14000 1 4 8 10 11 14 8 CD2 12 12 -0.14000 0 6 9 10 12 13 14 15 9 HD2 20 1 0.14000 1 3 12 13 14 10 CE1 12 12 -0.14000 0 5 11 12 13 14 15 11 HE1 20 1 0.14000 1 3 12 14 15 12 CE2 12 12 -0.14000 0 3 13 14 15 13 HE2 20 1 0.14000 1 2 14 15 14 CZ 12 12 -0.14000 0 1 15 15 HZ 20 1 0.14000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 16 C 12 12 0.45000 0 17 O 1 16 -0.45000 1 # bonds # NB 18 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 16 27 4 5 27 5 6 16 5 8 16 6 7 3 6 10 16 8 9 3 8 12 16 10 11 3 10 14 16 12 13 3 12 14 16 14 15 3 16 17 5 16 18 10 # bond angles # NBA 28 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 16 13 4 3 16 13 3 4 5 15 4 5 6 27 4 5 8 27 6 5 8 27 5 6 7 25 5 6 10 27 7 6 10 25 5 8 9 25 5 8 12 27 9 8 12 25 6 10 11 25 6 10 14 27 11 10 14 25 8 12 13 25 8 12 14 27 13 12 14 25 10 14 12 27 10 14 15 25 12 14 15 25 3 16 17 30 3 16 18 19 17 16 18 33 # improper dihedrals # NIDA 15 # IB JB KB LB MCB 1 -1 3 2 1 3 1 16 4 2 5 6 8 4 1 5 6 10 14 1 5 8 12 14 1 6 5 8 12 1 6 5 10 7 1 6 10 14 12 1 8 5 6 10 1 8 5 12 9 1 8 12 14 10 1 11 6 14 10 1 13 8 14 12 1 14 10 12 15 1 16 3 18 17 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 16 39 1 3 4 5 34 1 3 16 18 40 3 4 5 6 40 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 0.00000 1 5 2 3 4 5 6 2 CA 14 3 0.00000 0 6 3 4 5 6 7 8 3 CB 18 4 0.00000 1 3 4 5 6 4 CG 18 4 0.00000 0 1 5 5 CD 18 4 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 12 12 0.45000 0 7 O 1 16 -0.45000 1 # bonds # NB 8 # IB JB MCB 1 2 21 1 5 21 2 3 27 2 6 27 3 4 27 4 5 27 6 7 5 6 8 10 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 31 -1 1 5 31 2 1 5 21 1 2 3 13 1 2 6 13 3 2 6 13 2 3 4 13 3 4 5 13 1 5 4 13 2 6 7 30 2 6 8 19 7 6 8 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 2 5 1 2 1 6 3 2 6 2 8 7 1 # dihedrals # NDA 7 # IB JB KB LB MCB -2 -1 1 2 14 -1 1 2 6 39 2 1 5 4 39 1 2 3 4 34 1 2 6 8 40 2 3 4 5 34 3 4 5 1 34 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 7 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 1 5 4 5 7 8 9 4 CB 15 4 0.26600 0 3 5 6 7 5 OG 3 16 -0.67400 0 1 6 6 HG 21 1 0.40800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 7 C 12 12 0.45000 0 8 O 1 16 -0.45000 1 # bonds # NB 8 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 7 27 4 5 18 5 6 1 7 8 5 7 9 10 # bond angles # NBA 11 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 7 13 4 3 7 13 3 4 5 13 4 5 6 12 3 7 8 30 3 7 9 19 8 7 9 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 7 4 2 7 3 9 8 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 39 1 3 4 5 34 1 3 7 9 40 3 4 5 6 23 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 8 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 1 6 4 5 7 8 9 10 4 CB 14 3 0.26600 0 4 5 6 7 8 5 OG1 3 16 -0.67400 0 2 6 7 6 HG1 21 1 0.40800 1 0 7 CG2 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 8 27 4 5 18 4 7 27 5 6 1 8 9 5 8 10 10 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 13 3 4 7 15 5 4 7 15 4 5 6 12 3 8 9 30 3 8 10 19 9 8 10 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 8 4 2 4 5 7 3 2 8 3 10 9 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 39 1 3 4 5 34 1 3 8 10 40 3 4 5 6 23 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 20 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 20 21 22 4 CB 15 4 0.00000 1 8 5 6 7 8 9 11 12 20 5 CG 12 12 -0.21000 0 10 6 7 8 9 10 11 12 13 14 16 6 CD1 12 12 -0.14000 0 7 7 8 9 10 11 12 14 7 HD1 20 1 0.14000 0 4 8 9 10 11 8 CD2 12 12 0.00000 0 10 9 10 11 12 13 14 15 16 17 18 9 NE1 9 14 -0.10000 0 6 10 11 12 14 15 18 10 HE1 21 1 0.31000 0 2 11 14 11 CE2 12 12 0.00000 1 7 12 13 14 15 16 18 19 12 CE3 12 12 -0.14000 0 6 13 14 16 17 18 19 13 HE3 20 1 0.14000 1 3 16 17 18 14 CZ2 12 12 -0.14000 0 5 15 16 17 18 19 15 HZ2 20 1 0.14000 1 3 16 18 19 16 CZ3 12 12 -0.14000 0 3 17 18 19 17 HZ3 20 1 0.14000 1 2 18 19 18 CH2 12 12 -0.14000 0 1 19 19 HH2 20 1 0.14000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 20 C 12 12 0.45000 0 21 O 1 16 -0.45000 1 # bonds # NB 23 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 20 27 4 5 27 5 6 10 5 8 16 6 7 3 6 9 10 8 11 16 8 12 16 9 10 2 9 11 10 11 14 16 12 13 3 12 16 16 14 15 3 14 18 16 16 17 3 16 18 16 18 19 3 20 21 5 20 22 10 # bond angles # NBA 37 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 20 13 4 3 20 13 3 4 5 15 4 5 6 37 4 5 8 37 6 5 8 7 5 6 7 36 5 6 9 7 7 6 9 36 5 8 11 7 5 8 12 39 11 8 12 27 6 9 10 36 6 9 11 7 10 9 11 36 8 11 9 7 8 11 14 27 9 11 14 39 8 12 13 25 8 12 16 27 13 12 16 25 11 14 15 25 11 14 18 27 15 14 18 25 12 16 17 25 12 16 18 27 17 16 18 25 14 18 16 27 14 18 19 25 16 18 19 25 3 20 21 30 3 20 22 19 21 20 22 33 # improper dihedrals # NIDA 23 # IB JB KB LB MCB 1 -1 3 2 1 3 1 20 4 2 5 6 8 4 1 5 6 9 11 1 5 8 11 9 1 6 5 8 11 1 6 5 9 7 1 6 9 11 8 1 8 5 6 9 1 8 11 12 5 1 8 11 14 18 1 8 12 16 18 1 9 6 11 10 1 11 8 12 16 1 11 8 14 9 1 11 14 18 16 1 12 8 11 14 1 12 8 16 13 1 12 16 18 14 1 14 11 18 15 1 16 12 18 17 1 18 14 16 19 1 20 3 22 21 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 20 39 1 3 4 5 34 1 3 20 22 40 3 4 5 8 40 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 17 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 17 18 19 4 CB 15 4 0.00000 0 8 5 6 7 8 9 10 12 17 5 CG 12 12 0.00000 1 9 6 7 8 9 10 11 12 13 14 6 CD1 12 12 -0.14000 0 8 7 8 9 10 11 12 14 15 7 HD1 20 1 0.14000 1 4 8 10 11 14 8 CD2 12 12 -0.14000 0 6 9 10 12 13 14 15 9 HD2 20 1 0.14000 1 3 12 13 14 10 CE1 12 12 -0.14000 0 5 11 12 13 14 15 11 HE1 20 1 0.14000 1 3 12 14 15 12 CE2 12 12 -0.14000 0 3 13 14 15 13 HE2 20 1 0.14000 1 2 14 15 14 CZ 12 12 0.20300 0 2 15 16 15 OH 3 16 -0.61100 0 1 16 16 HH 21 1 0.40800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 17 C 12 12 0.45000 0 18 O 1 16 -0.45000 1 # bonds # NB 19 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 17 27 4 5 27 5 6 16 5 8 16 6 7 3 6 10 16 8 9 3 8 12 16 10 11 3 10 14 16 12 13 3 12 14 16 14 15 13 15 16 1 17 18 5 17 19 10 # bond angles # NBA 29 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 17 13 4 3 17 13 3 4 5 15 4 5 6 27 4 5 8 27 6 5 8 27 5 6 7 25 5 6 10 27 7 6 10 25 5 8 9 25 5 8 12 27 9 8 12 25 6 10 11 25 6 10 14 27 11 10 14 25 8 12 13 25 8 12 14 27 13 12 14 25 10 14 12 27 10 14 15 27 12 14 15 27 14 15 16 12 3 17 18 30 3 17 19 19 18 17 19 33 # improper dihedrals # NIDA 15 # IB JB KB LB MCB 1 -1 3 2 1 3 1 17 4 2 5 6 8 4 1 5 6 10 14 1 5 8 12 14 1 6 5 8 12 1 6 5 10 7 1 6 10 14 12 1 8 5 6 10 1 8 5 12 9 1 8 12 14 10 1 11 6 14 10 1 13 8 14 12 1 14 10 12 15 1 17 3 19 18 1 # dihedrals # NDA 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 17 39 1 3 4 5 34 1 3 17 19 40 3 4 5 6 40 10 14 15 16 11 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 7 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 6 4 5 6 7 8 9 4 CB 14 3 0.00000 0 3 5 6 7 5 CG1 16 5 0.00000 0 1 6 6 CG2 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 7 C 12 12 0.45000 0 8 O 1 16 -0.45000 1 # bonds # NB 8 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 7 27 4 5 27 4 6 27 7 8 5 7 9 10 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 7 13 4 3 7 13 3 4 5 15 3 4 6 15 5 4 6 15 3 7 8 30 3 7 9 19 8 7 9 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 7 4 2 3 5 6 4 2 7 3 9 8 1 # dihedrals # NDA 4 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 39 1 3 4 5 34 1 3 7 9 40 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 5 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 4 4 5 6 7 4 CB 16 5 0.00000 1 1 5 # trailing atoms #ATOM ANM IACM MASS CGMICGM 5 C 12 12 0.45000 0 6 O 1 16 -0.45000 1 # bonds # NB 6 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 5 27 5 6 5 5 7 10 # bond angles # NBA 9 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 5 13 4 3 5 13 3 5 6 30 3 5 7 19 6 5 7 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 4 1 5 3 2 5 3 7 6 1 # dihedrals # NDA 3 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 5 39 1 3 5 7 40 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 -0.31000 0 4 2 3 4 6 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 6 7 8 4 CB 15 4 0.00000 0 2 5 6 5 CG 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 12 12 0.45000 0 7 O 1 16 -0.45000 1 # bonds # NB 7 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 6 27 4 5 27 6 7 5 6 8 10 # bond angles # NBA 10 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 6 13 4 3 6 13 3 4 5 15 3 6 7 30 3 6 8 19 7 6 8 33 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 1 -1 3 2 1 3 1 6 4 2 6 3 8 7 1 # dihedrals # NDA 4 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 6 39 1 3 4 5 34 1 3 6 8 40 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 0.00000 0 4 2 3 4 13 2 CN 16 5 0.00000 1 1 3 3 CA 14 3 0.00000 1 6 4 5 7 13 14 15 4 CB 14 3 0.26600 0 6 5 6 7 8 9 13 5 OG1 3 16 -0.67400 0 2 6 7 6 HG1 21 1 0.40800 1 0 7 CG2 14 3 0.00000 0 3 8 9 10 8 CD1 16 5 0.00000 0 1 9 9 CD2 15 4 0.00000 1 2 10 11 10 CE 19 3 0.00000 0 2 11 12 11 CZ 19 3 0.00000 0 1 12 12 CH 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 13 C 12 12 0.45000 0 14 O 1 16 -0.45000 1 # bonds # NB 14 # IB JB MCB 1 2 21 1 3 21 3 4 27 3 13 27 4 5 18 4 7 27 5 6 1 7 8 27 7 9 27 9 10 27 10 11 10 11 12 27 13 14 5 13 15 10 # bond angles # NBA 19 # IB JB KB MCB -1 1 2 22 -1 1 3 31 2 1 3 30 1 3 4 13 1 3 13 13 4 3 13 13 3 4 5 13 3 4 7 15 5 4 7 15 4 5 6 12 4 7 8 15 4 7 9 15 8 7 9 15 7 9 10 15 9 10 11 27 10 11 12 27 3 13 14 30 3 13 15 19 14 13 15 33 # improper dihedrals # NIDA 5 # IB JB KB LB MCB 1 -1 3 2 1 3 1 13 4 2 4 5 7 3 2 7 8 9 4 2 13 3 15 14 1 # dihedrals # NDA 9 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 13 39 1 3 4 7 34 1 3 13 15 40 3 4 5 6 23 3 4 7 9 34 4 7 9 10 34 7 9 10 11 40 9 10 11 12 14 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 0.00000 0 4 2 3 4 8 2 CN 16 5 0.00000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 8 9 10 4 CB 15 4 0.00000 1 4 5 6 7 8 5 CG 14 3 0.00000 0 2 6 7 6 CD1 16 5 0.00000 0 1 7 7 CD2 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 8 C 12 12 0.45000 0 9 O 1 16 -0.45000 1 # bonds # NB 9 # IB JB MCB 1 2 21 1 3 21 3 4 27 3 8 27 4 5 27 5 6 27 5 7 27 8 9 5 8 10 10 # bond angles # NBA 13 # IB JB KB MCB -1 1 2 22 -1 1 3 31 2 1 3 30 1 3 4 13 1 3 8 13 4 3 8 13 3 4 5 15 4 5 6 15 4 5 7 15 6 5 7 15 3 8 9 30 3 8 10 19 9 8 10 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 8 4 2 4 6 7 5 2 8 3 10 9 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 39 1 3 4 5 34 1 3 8 10 40 3 4 5 6 34 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 0.00000 0 4 2 3 4 7 2 CN 16 5 0.00000 1 1 3 3 CA 14 3 0.00000 0 6 4 5 6 7 8 9 4 CB 14 3 0.00000 0 3 5 6 7 5 CG1 16 5 0.00000 0 1 6 6 CG2 16 5 0.00000 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 7 C 12 12 0.45000 0 8 O 1 16 -0.45000 1 # bonds # NB 8 # IB JB MCB 1 2 21 1 3 21 3 4 27 3 7 27 4 5 27 4 6 27 7 8 5 7 9 10 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 22 -1 1 3 31 2 1 3 30 1 3 4 13 1 3 7 13 4 3 7 13 3 4 5 15 3 4 6 15 5 4 6 15 3 7 8 30 3 7 9 19 8 7 9 33 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 -1 3 2 1 3 1 7 4 2 3 5 6 4 2 7 3 9 8 1 # dihedrals # NDA 4 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 39 1 3 4 5 34 1 3 7 9 40 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 6 14 0.00000 0 3 2 3 4 2 CN 16 5 0.00000 1 1 3 3 CA 15 4 0.00000 1 3 4 5 6 # trailing atoms #ATOM ANM IACM MASS CGMICGM 4 C 12 12 0.45000 0 5 O 1 16 -0.45000 1 # bonds # NB 5 # IB JB MCB 1 2 21 1 3 21 3 4 27 4 5 5 4 6 10 # bond angles # NBA 7 # IB JB KB MCB -1 1 2 22 -1 1 3 31 2 1 3 30 1 3 4 13 3 4 5 30 3 4 6 19 5 4 6 33 # improper dihedrals # NIDA 2 # IB JB KB LB MCB 1 -1 3 2 1 4 3 6 5 1 # dihedrals # NDA 3 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 4 39 1 3 4 6 40 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE DADE # building block (residue, nucleotide, etc.) # RNME DADE # number of atoms, number of preceding exclusions # NMAT NLIN 25 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 30 31 0.99000 0 4 2 3 4 5 2 O1P 2 16 -0.63500 0 2 3 4 3 O2P 2 16 -0.63500 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 15 4 0.00000 1 3 6 7 24 6 C4* 14 3 0.16000 0 5 7 8 23 24 25 7 O4* 3 16 -0.36000 0 4 8 9 23 24 8 C1* 14 3 0.20000 1 9 9 10 11 19 20 21 22 23 24 9 N9 9 14 -0.20000 0 9 10 11 12 15 19 20 21 22 23 10 C4 12 12 0.20000 1 10 11 12 13 14 15 16 19 20 21 22 11 N3 9 14 -0.54000 0 7 12 13 14 15 19 20 21 12 C2 12 12 0.44000 0 5 13 14 15 16 19 13 H2 20 1 0.10000 1 2 14 15 14 N1 9 14 -0.54000 0 4 15 16 19 20 15 C6 12 12 0.54000 1 6 16 17 18 19 20 21 16 N6 7 14 -0.83000 0 4 17 18 19 20 17 H61 21 1 0.41500 0 2 18 20 18 H62 21 1 0.41500 1 1 20 19 C5 12 12 0.00000 0 3 20 21 22 20 N7 9 14 -0.54000 0 2 21 22 21 C8 12 12 0.44000 0 1 22 22 H8 20 1 0.10000 1 0 23 C2* 18 4 0.00000 0 2 24 25 # trailing atoms #ATOM ANM IACM MASS CGMICGM 24 C3* 14 3 0.00000 1 25 O3* 3 16 -0.36000 0 # bonds # NB 28 # IB JB MCB 1 2 24 1 3 24 1 4 28 4 5 20 5 6 26 6 7 20 6 24 26 7 8 20 8 9 22 8 23 26 9 10 10 9 21 10 10 11 12 10 19 16 11 12 7 12 13 3 12 14 7 14 15 12 15 16 9 15 19 16 16 17 2 16 18 2 19 20 10 20 21 10 21 22 3 23 24 26 24 25 20 25 26 28 # bond angles # NBA 44 # IB JB KB MCB 0 1 2 14 0 1 3 14 0 1 4 5 2 1 3 29 2 1 4 14 3 1 4 14 1 4 5 26 4 5 6 9 5 6 7 9 5 6 24 8 7 6 24 9 6 7 8 10 7 8 9 9 7 8 23 9 9 8 23 9 8 9 10 37 8 9 21 37 10 9 21 7 9 10 11 39 9 10 19 7 11 10 19 27 10 11 12 27 11 12 13 25 11 12 14 27 13 12 14 25 12 14 15 27 14 15 16 27 14 15 19 27 16 15 19 27 15 16 17 23 15 16 18 23 17 16 18 24 10 19 15 27 10 19 20 7 15 19 20 39 19 20 21 7 9 21 20 7 9 21 22 36 20 21 22 36 8 23 24 8 6 24 23 8 6 24 25 9 23 24 25 9 24 25 26 26 # improper dihedrals # NIDA 21 # IB JB KB LB MCB 8 10 21 9 1 9 10 19 20 1 10 9 11 19 1 10 9 21 20 1 10 11 12 14 1 10 19 20 21 1 11 10 19 15 1 11 12 14 15 1 12 11 13 14 1 12 14 15 19 1 14 15 19 10 1 16 14 19 15 1 16 17 18 15 1 19 10 11 12 1 19 15 20 10 1 19 20 21 9 1 21 9 10 19 1 21 9 20 22 1 23 7 9 8 2 24 5 7 6 2 24 23 25 6 2 # dihedrals # NDA 23 # IB JB KB LB MCB -1 0 1 4 20 -1 0 1 4 27 0 1 4 5 20 0 1 4 5 27 1 4 5 6 7 1 4 5 6 22 4 5 6 7 8 4 5 6 7 25 4 5 6 24 17 4 5 6 24 34 24 6 7 8 29 5 6 24 23 34 5 6 24 25 17 7 6 24 23 17 7 6 24 25 18 6 7 8 23 29 7 8 9 10 16 7 8 23 24 17 7 8 23 24 34 19 15 16 17 14 8 23 24 6 34 8 23 24 25 17 6 24 25 26 29 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE DGUA # building block (residue, nucleotide, etc.) # RNME DGUA # number of atoms, number of preceding exclusions # NMAT NLIN 26 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 30 31 0.99000 0 4 2 3 4 5 2 O1P 2 16 -0.63500 0 2 3 4 3 O2P 2 16 -0.63500 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 15 4 0.00000 1 3 6 7 25 6 C4* 14 3 0.16000 0 5 7 8 24 25 26 7 O4* 3 16 -0.36000 0 4 8 9 24 25 8 C1* 14 3 0.20000 1 9 9 10 11 20 21 22 23 24 25 9 N9 9 14 -0.20000 0 9 10 11 12 18 20 21 22 23 24 10 C4 12 12 0.20000 1 10 11 12 13 16 18 19 20 21 22 23 11 N3 9 14 -0.54000 0 8 12 13 16 17 18 20 21 22 12 C2 12 12 0.54000 1 8 13 14 15 16 17 18 19 20 13 N2 7 14 -0.83000 0 5 14 15 16 17 18 14 H21 21 1 0.41500 0 1 15 15 H22 21 1 0.41500 1 0 16 N1 9 14 -0.31000 0 5 17 18 19 20 21 17 H1 21 1 0.31000 1 3 18 19 20 18 C6 12 12 0.45000 0 4 19 20 21 22 19 O6 1 16 -0.45000 1 2 20 21 20 C5 12 12 0.00000 0 3 21 22 23 21 N7 9 14 -0.54000 0 2 22 23 22 C8 12 12 0.44000 0 1 23 23 H8 20 1 0.10000 1 0 24 C2* 18 4 0.00000 0 2 25 26 # trailing atoms #ATOM ANM IACM MASS CGMICGM 25 C3* 14 3 0.00000 1 26 O3* 3 16 -0.36000 0 # bonds # NB 29 # IB JB MCB 1 2 24 1 3 24 1 4 28 4 5 20 5 6 26 6 7 20 6 25 26 7 8 20 8 9 22 8 24 26 9 10 10 9 22 10 10 11 12 10 20 16 11 12 12 12 13 9 12 16 17 13 14 2 13 15 2 16 17 2 16 18 17 18 19 5 18 20 16 20 21 10 21 22 10 22 23 3 24 25 26 25 26 20 26 27 28 # bond angles # NBA 46 # IB JB KB MCB 0 1 2 14 0 1 3 14 0 1 4 5 2 1 3 29 2 1 4 14 3 1 4 14 1 4 5 26 4 5 6 9 5 6 7 9 5 6 25 8 7 6 25 9 6 7 8 10 7 8 9 9 7 8 24 9 9 8 24 9 8 9 10 37 8 9 22 37 10 9 22 7 9 10 11 39 9 10 20 7 11 10 20 27 10 11 12 27 11 12 13 27 11 12 16 27 13 12 16 27 12 13 14 23 12 13 15 23 14 13 15 24 12 16 17 25 12 16 18 27 17 16 18 25 16 18 19 27 16 18 20 27 19 18 20 27 10 20 18 27 10 20 21 7 18 20 21 39 20 21 22 7 9 22 21 7 9 22 23 36 21 22 23 36 8 24 25 8 6 25 24 8 6 25 26 9 24 25 26 9 25 26 27 26 # improper dihedrals # NIDA 22 # IB JB KB LB MCB 8 10 22 9 1 9 10 20 21 1 10 9 11 20 1 10 9 22 21 1 10 11 12 16 1 10 20 21 22 1 11 10 20 18 1 11 12 16 18 1 12 16 18 20 1 13 11 16 12 1 13 14 15 12 1 16 18 20 10 1 17 12 18 16 1 19 16 20 18 1 20 10 11 12 1 20 18 21 10 1 20 21 22 9 1 22 9 10 20 1 22 9 21 23 1 24 7 9 8 2 25 5 7 6 2 25 24 26 6 2 # dihedrals # NDA 23 # IB JB KB LB MCB -1 0 1 4 20 -1 0 1 4 27 0 1 4 5 20 0 1 4 5 27 1 4 5 6 7 1 4 5 6 22 4 5 6 7 8 4 5 6 7 25 4 5 6 25 17 4 5 6 25 34 25 6 7 8 29 5 6 25 24 34 5 6 25 26 17 7 6 25 24 17 7 6 25 26 18 6 7 8 24 29 7 8 9 10 16 7 8 24 25 17 7 8 24 25 34 11 12 13 14 14 8 24 25 6 34 8 24 25 26 17 6 25 26 27 29 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE DCYT # building block (residue, nucleotide, etc.) # RNME DCYT # number of atoms, number of preceding exclusions # NMAT NLIN 23 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 30 31 0.99000 0 4 2 3 4 5 2 O1P 2 16 -0.63500 0 2 3 4 3 O2P 2 16 -0.63500 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 15 4 0.00000 1 3 6 7 22 6 C4* 14 3 0.16000 0 5 7 8 21 22 23 7 O4* 3 16 -0.36000 0 4 8 9 21 22 8 C1* 14 3 0.20000 1 9 9 10 11 12 13 14 19 21 22 9 N1 9 14 -0.20000 0 9 10 11 12 13 14 15 19 20 21 10 C6 12 12 0.10000 0 8 11 12 13 14 15 16 19 20 11 H6 20 1 0.10000 1 4 12 15 19 20 12 C2 12 12 0.45000 0 5 13 14 15 16 19 13 O2 1 16 -0.45000 1 2 14 15 14 N3 9 14 -0.54000 0 4 15 16 19 20 15 C4 12 12 0.54000 1 5 16 17 18 19 20 16 N4 7 14 -0.83000 0 4 17 18 19 20 17 H41 21 1 0.41500 0 1 18 18 H42 21 1 0.41500 1 0 19 C5 12 12 -0.10000 0 1 20 20 H5 20 1 0.10000 1 0 21 C2* 18 4 0.00000 0 2 22 23 # trailing atoms #ATOM ANM IACM MASS CGMICGM 22 C3* 14 3 0.00000 1 23 O3* 3 16 -0.36000 0 # bonds # NB 25 # IB JB MCB 1 2 24 1 3 24 1 4 28 4 5 20 5 6 26 6 7 20 6 22 26 7 8 20 8 9 23 8 21 26 9 10 17 9 12 17 10 11 3 10 19 16 12 13 5 12 14 12 14 15 12 15 16 9 15 19 16 16 17 2 16 18 2 19 20 3 21 22 26 22 23 20 23 24 28 # bond angles # NBA 39 # IB JB KB MCB 0 1 2 14 0 1 3 14 0 1 4 5 2 1 3 29 2 1 4 14 3 1 4 14 1 4 5 26 4 5 6 9 5 6 7 9 5 6 22 8 7 6 22 9 6 7 8 10 7 8 9 9 7 8 21 9 9 8 21 8 8 9 10 27 8 9 12 27 10 9 12 27 9 10 11 25 9 10 19 27 11 10 19 25 9 12 13 27 9 12 14 27 13 12 14 27 12 14 15 27 14 15 16 27 14 15 19 27 16 15 19 27 15 16 17 23 15 16 18 23 17 16 18 24 10 19 15 27 10 19 20 25 15 19 20 25 8 21 22 8 6 22 21 8 6 22 23 9 21 22 23 9 22 23 24 26 # improper dihedrals # NIDA 15 # IB JB KB LB MCB 9 10 12 8 1 9 10 19 15 1 9 12 14 15 1 10 9 12 14 1 10 9 19 11 1 12 9 10 19 1 12 14 15 19 1 13 9 14 12 1 14 15 19 10 1 16 14 19 15 1 16 17 18 15 1 19 10 15 20 1 21 7 9 8 2 22 5 7 6 2 22 21 23 6 2 # dihedrals # NDA 23 # IB JB KB LB MCB -1 0 1 4 20 -1 0 1 4 27 0 1 4 5 20 0 1 4 5 27 1 4 5 6 7 1 4 5 6 22 4 5 6 7 8 4 5 6 7 25 4 5 6 22 17 4 5 6 22 34 22 6 7 8 29 5 6 22 21 34 5 6 22 23 17 7 6 22 21 17 7 6 22 23 18 6 7 8 21 29 7 8 9 12 16 7 8 21 22 17 7 8 21 22 34 14 15 16 17 14 8 21 22 6 34 8 21 22 23 17 6 22 23 24 29 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE DTHY # building block (residue, nucleotide, etc.) # RNME DTHY # number of atoms, number of preceding exclusions # NMAT NLIN 22 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 30 31 0.99000 0 4 2 3 4 5 2 O1P 2 16 -0.63500 0 2 3 4 3 O2P 2 16 -0.63500 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 15 4 0.00000 1 3 6 7 21 6 C4* 14 3 0.16000 0 5 7 8 20 21 22 7 O4* 3 16 -0.36000 0 4 8 9 20 21 8 C1* 14 3 0.20000 1 9 9 10 11 12 13 14 18 20 21 9 N1 9 14 -0.20000 0 10 10 11 12 13 14 15 16 18 19 20 10 C6 12 12 0.10000 0 8 11 12 13 14 16 17 18 19 11 H6 20 1 0.10000 1 4 12 16 18 19 12 C2 12 12 0.45000 0 6 13 14 15 16 17 18 13 O2 1 16 -0.45000 1 3 14 15 16 14 N3 9 14 -0.31000 0 5 15 16 17 18 19 15 H3 21 1 0.31000 1 3 16 17 18 16 C4 12 12 0.45000 0 3 17 18 19 17 O4 1 16 -0.45000 1 2 18 19 18 C5 12 12 0.00000 0 1 19 19 C5M 16 5 0.00000 1 0 20 C2* 18 4 0.00000 0 2 21 22 # trailing atoms #ATOM ANM IACM MASS CGMICGM 21 C3* 14 3 0.00000 1 22 O3* 3 16 -0.36000 0 # bonds # NB 24 # IB JB MCB 1 2 24 1 3 24 1 4 28 4 5 20 5 6 26 6 7 20 6 21 26 7 8 20 8 9 23 8 20 26 9 10 17 9 12 17 10 11 3 10 18 16 12 13 5 12 14 17 14 15 2 14 16 17 16 17 5 16 18 16 18 19 27 20 21 26 21 22 20 22 23 28 # bond angles # NBA 38 # IB JB KB MCB 0 1 2 14 0 1 3 14 0 1 4 5 2 1 3 29 2 1 4 14 3 1 4 14 1 4 5 26 4 5 6 9 5 6 7 9 5 6 21 8 7 6 21 9 6 7 8 10 7 8 9 9 7 8 20 9 9 8 20 8 8 9 10 27 8 9 12 27 10 9 12 27 9 10 11 25 9 10 18 27 11 10 18 25 9 12 13 27 9 12 14 27 13 12 14 27 12 14 15 25 12 14 16 27 15 14 16 25 14 16 17 27 14 16 18 27 17 16 18 27 10 18 16 27 10 18 19 27 16 18 19 27 8 20 21 8 6 21 20 8 6 21 22 9 20 21 22 9 21 22 23 26 # improper dihedrals # NIDA 15 # IB JB KB LB MCB 9 10 12 8 1 9 10 18 16 1 9 12 14 16 1 10 9 12 14 1 10 9 18 11 1 12 9 10 18 1 12 14 16 18 1 13 9 14 12 1 14 16 18 10 1 15 12 16 14 1 17 14 18 16 1 18 10 16 19 1 20 7 9 8 2 21 5 7 6 2 21 20 22 6 2 # dihedrals # NDA 22 # IB JB KB LB MCB -1 0 1 4 20 -1 0 1 4 27 0 1 4 5 20 0 1 4 5 27 1 4 5 6 7 1 4 5 6 22 4 5 6 7 8 4 5 6 7 25 4 5 6 21 17 4 5 6 21 34 21 6 7 8 29 5 6 21 20 34 5 6 21 22 17 7 6 21 20 17 7 6 21 22 18 6 7 8 20 29 7 8 9 12 16 7 8 20 21 17 7 8 20 21 34 8 20 21 6 34 8 20 21 22 17 6 21 22 23 29 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE ADE # building block (residue, nucleotide, etc.) # RNME ADE # number of atoms, number of preceding exclusions # NMAT NLIN 27 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 30 31 0.99000 0 4 2 3 4 5 2 O1P 2 16 -0.63500 0 2 3 4 3 O2P 2 16 -0.63500 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 15 4 0.00000 1 3 6 7 26 6 C4* 14 3 0.16000 0 5 7 8 23 26 27 7 O4* 3 16 -0.36000 0 4 8 9 23 26 8 C1* 14 3 0.20000 1 10 9 10 11 19 20 21 22 23 24 26 9 N9 9 14 -0.20000 0 9 10 11 12 15 19 20 21 22 23 10 C4 12 12 0.20000 1 10 11 12 13 14 15 16 19 20 21 22 11 N3 9 14 -0.54000 0 7 12 13 14 15 19 20 21 12 C2 12 12 0.44000 0 5 13 14 15 16 19 13 H2 20 1 0.10000 1 2 14 15 14 N1 9 14 -0.54000 0 4 15 16 19 20 15 C6 12 12 0.54000 1 6 16 17 18 19 20 21 16 N6 7 14 -0.83000 0 4 17 18 19 20 17 H61 21 1 0.41500 0 2 18 20 18 H62 21 1 0.41500 1 1 20 19 C5 12 12 0.00000 0 3 20 21 22 20 N7 9 14 -0.54000 0 2 21 22 21 C8 12 12 0.44000 0 1 22 22 H8 20 1 0.10000 1 0 23 C2* 14 3 0.15000 0 4 24 25 26 27 24 O2* 3 16 -0.54800 0 2 25 26 25 H2* 21 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 26 C3* 14 3 0.00000 1 27 O3* 3 16 -0.36000 0 # bonds # NB 30 # IB JB MCB 1 2 24 1 3 24 1 4 28 4 5 20 5 6 26 6 7 20 6 26 26 7 8 20 8 9 22 8 23 26 9 10 10 9 21 10 10 11 12 10 19 16 11 12 7 12 13 3 12 14 7 14 15 12 15 16 9 15 19 16 16 17 2 16 18 2 19 20 10 20 21 10 21 22 3 23 24 20 23 26 26 24 25 1 26 27 20 27 28 28 # bond angles # NBA 47 # IB JB KB MCB 0 1 2 14 0 1 3 14 0 1 4 5 2 1 3 29 2 1 4 14 3 1 4 14 1 4 5 26 4 5 6 9 5 6 7 9 5 6 26 8 7 6 26 9 6 7 8 10 7 8 9 9 7 8 23 9 9 8 23 9 8 9 10 37 8 9 21 37 10 9 21 7 9 10 11 39 9 10 19 7 11 10 19 27 10 11 12 27 11 12 13 25 11 12 14 27 13 12 14 25 12 14 15 27 14 15 16 27 14 15 19 27 16 15 19 27 15 16 17 23 15 16 18 23 17 16 18 24 10 19 15 27 10 19 20 7 15 19 20 39 19 20 21 7 9 21 20 7 9 21 22 36 20 21 22 36 8 23 24 9 8 23 26 8 24 23 26 9 23 24 25 12 6 26 23 8 6 26 27 9 23 26 27 9 26 27 28 26 # improper dihedrals # NIDA 22 # IB JB KB LB MCB 8 10 21 9 1 9 10 19 20 1 10 9 11 19 1 10 9 21 20 1 10 11 12 14 1 10 19 20 21 1 11 10 19 15 1 11 12 14 15 1 12 11 13 14 1 12 14 15 19 1 14 15 19 10 1 16 14 19 15 1 16 17 18 15 1 19 10 11 12 1 19 15 20 10 1 19 20 21 9 1 21 9 10 19 1 21 9 20 22 1 23 7 9 8 2 23 24 26 8 2 26 5 7 6 2 26 23 27 6 2 # dihedrals # NDA 28 # IB JB KB LB MCB -1 0 1 4 20 -1 0 1 4 27 0 1 4 5 20 0 1 4 5 27 1 4 5 6 7 1 4 5 6 22 4 5 6 7 8 4 5 6 7 25 4 5 6 26 17 4 5 6 26 34 26 6 7 8 29 5 6 26 23 34 5 6 26 27 17 7 6 26 23 17 7 6 26 27 18 6 7 8 23 29 7 8 9 10 16 7 8 23 24 18 7 8 23 26 17 7 8 23 26 34 9 8 23 24 17 19 15 16 17 14 8 23 24 25 23 8 23 26 6 34 8 23 26 27 17 24 23 26 6 17 24 23 26 27 18 6 26 27 28 29 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE GUA # building block (residue, nucleotide, etc.) # RNME GUA # number of atoms, number of preceding exclusions # NMAT NLIN 28 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 30 31 0.99000 0 4 2 3 4 5 2 O1P 2 16 -0.63500 0 2 3 4 3 O2P 2 16 -0.63500 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 15 4 0.00000 1 3 6 7 27 6 C4* 14 3 0.16000 0 5 7 8 24 27 28 7 O4* 3 16 -0.36000 0 4 8 9 24 27 8 C1* 14 3 0.20000 1 10 9 10 11 20 21 22 23 24 25 27 9 N9 9 14 -0.20000 0 9 10 11 12 18 20 21 22 23 24 10 C4 12 12 0.20000 1 10 11 12 13 16 18 19 20 21 22 23 11 N3 9 14 -0.54000 0 8 12 13 16 17 18 20 21 22 12 C2 12 12 0.54000 1 8 13 14 15 16 17 18 19 20 13 N2 7 14 -0.83000 0 5 14 15 16 17 18 14 H21 21 1 0.41500 0 1 15 15 H22 21 1 0.41500 1 0 16 N1 9 14 -0.31000 0 5 17 18 19 20 21 17 H1 21 1 0.31000 1 3 18 19 20 18 C6 12 12 0.45000 0 4 19 20 21 22 19 O6 1 16 -0.45000 1 2 20 21 20 C5 12 12 0.00000 0 3 21 22 23 21 N7 9 14 -0.54000 0 2 22 23 22 C8 12 12 0.44000 0 1 23 23 H8 20 1 0.10000 1 0 24 C2* 14 3 0.15000 0 4 25 26 27 28 25 O2* 3 16 -0.54800 0 2 26 27 26 H2* 21 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 27 C3* 14 3 0.00000 1 28 O3* 3 16 -0.36000 0 # bonds # NB 31 # IB JB MCB 1 2 24 1 3 24 1 4 28 4 5 20 5 6 26 6 7 20 6 27 26 7 8 20 8 9 22 8 24 26 9 10 10 9 22 10 10 11 12 10 20 16 11 12 12 12 13 9 12 16 17 13 14 2 13 15 2 16 17 2 16 18 17 18 19 5 18 20 16 20 21 10 21 22 10 22 23 3 24 25 20 24 27 26 25 26 1 27 28 20 28 29 28 # bond angles # NBA 49 # IB JB KB MCB 0 1 2 14 0 1 3 14 0 1 4 5 2 1 3 29 2 1 4 14 3 1 4 14 1 4 5 26 4 5 6 9 5 6 7 9 5 6 27 8 7 6 27 9 6 7 8 10 7 8 9 9 7 8 24 9 9 8 24 9 8 9 10 37 8 9 22 37 10 9 22 7 9 10 11 39 9 10 20 7 11 10 20 27 10 11 12 27 11 12 13 27 11 12 16 27 13 12 16 27 12 13 14 23 12 13 15 23 14 13 15 24 12 16 17 25 12 16 18 27 17 16 18 25 16 18 19 27 16 18 20 27 19 18 20 27 10 20 18 27 10 20 21 7 18 20 21 39 20 21 22 7 9 22 21 7 9 22 23 36 21 22 23 36 8 24 25 9 8 24 27 8 25 24 27 9 24 25 26 12 6 27 24 8 6 27 28 9 24 27 28 9 27 28 29 26 # improper dihedrals # NIDA 23 # IB JB KB LB MCB 8 10 22 9 1 9 10 20 21 1 10 9 11 20 1 10 9 22 21 1 10 11 12 16 1 10 20 21 22 1 11 10 20 18 1 11 12 16 18 1 12 16 18 20 1 13 11 16 12 1 13 14 15 12 1 16 18 20 10 1 17 12 18 16 1 19 16 20 18 1 20 10 11 12 1 20 18 21 10 1 20 21 22 9 1 22 9 10 20 1 22 9 21 23 1 24 7 9 8 2 24 25 27 8 2 27 5 7 6 2 27 24 28 6 2 # dihedrals # NDA 28 # IB JB KB LB MCB -1 0 1 4 20 -1 0 1 4 27 0 1 4 5 20 0 1 4 5 27 1 4 5 6 7 1 4 5 6 22 4 5 6 7 8 4 5 6 7 25 4 5 6 27 17 4 5 6 27 34 27 6 7 8 29 5 6 27 24 34 5 6 27 28 17 7 6 27 24 17 7 6 27 28 18 6 7 8 24 29 7 8 9 10 16 7 8 24 25 18 7 8 24 27 17 7 8 24 27 34 9 8 24 25 17 11 12 13 14 14 8 24 25 26 23 8 24 27 6 34 8 24 27 28 17 25 24 27 6 17 25 24 27 28 18 6 27 28 29 29 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE CYT # building block (residue, nucleotide, etc.) # RNME CYT # number of atoms, number of preceding exclusions # NMAT NLIN 25 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 30 31 0.99000 0 4 2 3 4 5 2 O1P 2 16 -0.63500 0 2 3 4 3 O2P 2 16 -0.63500 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 15 4 0.00000 1 3 6 7 24 6 C4* 14 3 0.16000 0 5 7 8 21 24 25 7 O4* 3 16 -0.36000 0 4 8 9 21 24 8 C1* 14 3 0.20000 1 10 9 10 11 12 13 14 19 21 22 24 9 N1 9 14 -0.20000 0 9 10 11 12 13 14 15 19 20 21 10 C6 12 12 0.10000 0 8 11 12 13 14 15 16 19 20 11 H6 20 1 0.10000 1 4 12 15 19 20 12 C2 12 12 0.45000 0 5 13 14 15 16 19 13 O2 1 16 -0.45000 1 2 14 15 14 N3 9 14 -0.54000 0 4 15 16 19 20 15 C4 12 12 0.54000 1 5 16 17 18 19 20 16 N4 7 14 -0.83000 0 4 17 18 19 20 17 H41 21 1 0.41500 0 1 18 18 H42 21 1 0.41500 1 0 19 C5 12 12 -0.10000 0 1 20 20 H5 20 1 0.10000 1 0 21 C2* 14 3 0.15000 0 4 22 23 24 25 22 O2* 3 16 -0.54800 0 2 23 24 23 H2* 21 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 24 C3* 14 3 0.00000 1 25 O3* 3 16 -0.36000 0 # bonds # NB 27 # IB JB MCB 1 2 24 1 3 24 1 4 28 4 5 20 5 6 26 6 7 20 6 24 26 7 8 20 8 9 23 8 21 26 9 10 17 9 12 17 10 11 3 10 19 16 12 13 5 12 14 12 14 15 12 15 16 9 15 19 16 16 17 2 16 18 2 19 20 3 21 22 20 21 24 26 22 23 1 24 25 20 25 26 28 # bond angles # NBA 42 # IB JB KB MCB 0 1 2 14 0 1 3 14 0 1 4 5 2 1 3 29 2 1 4 14 3 1 4 14 1 4 5 26 4 5 6 9 5 6 7 9 5 6 24 8 7 6 24 9 6 7 8 10 7 8 9 9 7 8 21 9 9 8 21 8 8 9 10 27 8 9 12 27 10 9 12 27 9 10 11 25 9 10 19 27 11 10 19 25 9 12 13 27 9 12 14 27 13 12 14 27 12 14 15 27 14 15 16 27 14 15 19 27 16 15 19 27 15 16 17 23 15 16 18 23 17 16 18 24 10 19 15 27 10 19 20 25 15 19 20 25 8 21 22 9 8 21 24 8 22 21 24 9 21 22 23 12 6 24 21 8 6 24 25 9 21 24 25 9 24 25 26 26 # improper dihedrals # NIDA 16 # IB JB KB LB MCB 9 10 12 8 1 9 10 19 15 1 9 12 14 15 1 10 9 12 14 1 10 9 19 11 1 12 9 10 19 1 12 14 15 19 1 13 9 14 12 1 14 15 19 10 1 16 14 19 15 1 16 17 18 15 1 19 10 15 20 1 21 7 9 8 2 21 22 24 8 2 24 5 7 6 2 24 21 25 6 2 # dihedrals # NDA 28 # IB JB KB LB MCB -1 0 1 4 20 -1 0 1 4 27 0 1 4 5 20 0 1 4 5 27 1 4 5 6 7 1 4 5 6 22 4 5 6 7 8 4 5 6 7 25 4 5 6 24 17 4 5 6 24 34 24 6 7 8 29 5 6 24 21 34 5 6 24 25 17 7 6 24 21 17 7 6 24 25 18 6 7 8 21 29 7 8 9 12 16 7 8 21 22 18 7 8 21 24 17 7 8 21 24 34 9 8 21 22 17 14 15 16 17 14 8 21 22 23 23 8 21 24 6 34 8 21 24 25 17 22 21 24 6 17 22 21 24 25 18 6 24 25 26 29 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE URA # building block (residue, nucleotide, etc.) # RNME URA # number of atoms, number of preceding exclusions # NMAT NLIN 24 2 # preceding exclusions #ATOM MAE MSAE -1 2 0 1 0 4 1 2 3 4 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 P 30 31 0.99000 0 4 2 3 4 5 2 O1P 2 16 -0.63500 0 2 3 4 3 O2P 2 16 -0.63500 0 1 4 4 O5* 3 16 -0.36000 1 2 5 6 5 C5* 15 4 0.00000 1 3 6 7 23 6 C4* 14 3 0.16000 0 5 7 8 20 23 24 7 O4* 3 16 -0.36000 0 4 8 9 20 23 8 C1* 14 3 0.20000 1 10 9 10 11 12 13 14 18 20 21 23 9 N1 9 14 -0.20000 0 10 10 11 12 13 14 15 16 18 19 20 10 C6 12 12 0.10000 0 8 11 12 13 14 16 17 18 19 11 H6 20 1 0.10000 1 4 12 16 18 19 12 C2 12 12 0.45000 0 6 13 14 15 16 17 18 13 O2 1 16 -0.45000 1 3 14 15 16 14 N3 9 14 -0.31000 0 5 15 16 17 18 19 15 H3 21 1 0.31000 1 3 16 17 18 16 C4 12 12 0.45000 0 3 17 18 19 17 O4 1 16 -0.45000 1 2 18 19 18 C5 12 12 -0.10000 0 1 19 19 H5 20 1 0.10000 1 0 20 C2* 14 3 0.15000 0 4 21 22 23 24 21 O2* 3 16 -0.54800 0 2 22 23 22 H2* 21 1 0.39800 1 0 # trailing atoms #ATOM ANM IACM MASS CGMICGM 23 C3* 14 3 0.00000 1 24 O3* 3 16 -0.36000 0 # bonds # NB 26 # IB JB MCB 1 2 24 1 3 24 1 4 28 4 5 20 5 6 26 6 7 20 6 23 26 7 8 20 8 9 23 8 20 26 9 10 17 9 12 17 10 11 3 10 18 16 12 13 5 12 14 17 14 15 2 14 16 17 16 17 5 16 18 16 18 19 3 20 21 20 20 23 26 21 22 1 23 24 20 24 25 28 # bond angles # NBA 41 # IB JB KB MCB 0 1 2 14 0 1 3 14 0 1 4 5 2 1 3 29 2 1 4 14 3 1 4 14 1 4 5 26 4 5 6 9 5 6 7 9 5 6 23 8 7 6 23 9 6 7 8 10 7 8 9 9 7 8 20 9 9 8 20 8 8 9 10 27 8 9 12 27 10 9 12 27 9 10 11 25 9 10 18 27 11 10 18 25 9 12 13 27 9 12 14 27 13 12 14 27 12 14 15 25 12 14 16 27 15 14 16 25 14 16 17 27 14 16 18 27 17 16 18 27 10 18 16 27 10 18 19 25 16 18 19 25 8 20 21 9 8 20 23 8 21 20 23 9 20 21 22 12 6 23 20 8 6 23 24 9 20 23 24 9 23 24 25 26 # improper dihedrals # NIDA 16 # IB JB KB LB MCB 9 10 12 8 1 9 10 18 16 1 9 12 14 16 1 10 9 12 14 1 10 9 18 11 1 12 9 10 18 1 12 14 16 18 1 13 9 14 12 1 14 16 18 10 1 15 12 16 14 1 17 14 18 16 1 18 10 16 19 1 20 7 9 8 2 20 21 23 8 2 23 5 7 6 2 23 20 24 6 2 # dihedrals # NDA 27 # IB JB KB LB MCB -1 0 1 4 20 -1 0 1 4 27 0 1 4 5 20 0 1 4 5 27 1 4 5 6 7 1 4 5 6 22 4 5 6 7 8 4 5 6 7 25 4 5 6 23 17 4 5 6 23 34 23 6 7 8 29 5 6 23 20 34 5 6 23 24 17 7 6 23 20 17 7 6 23 24 18 6 7 8 20 29 7 8 9 12 16 7 8 20 21 18 7 8 20 23 17 7 8 20 23 34 9 8 20 21 17 8 20 21 22 23 8 20 23 6 34 8 20 23 24 17 21 20 23 6 17 21 20 23 24 18 6 23 24 25 29 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE DPPC # building block (residue, nucleotide, etc.) # RNME DPPC # number of atoms, number of preceding exclusions # NMAT NLIN 50 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C33 16 5 0.25000 0 4 2 3 4 5 2 C34 16 5 0.25000 0 3 3 4 5 3 C35 16 5 0.25000 0 2 4 5 4 N 8 14 0.00000 0 2 5 6 5 C32 15 4 0.25000 1 2 6 7 6 C31 15 4 0.00000 1 2 7 8 7 O32 3 16 -0.36000 0 4 8 9 10 11 8 P 30 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 15 4 0.00000 1 3 13 14 32 13 C2 14 3 0.16000 0 4 14 15 32 33 14 O21 4 16 -0.36000 0 4 15 16 17 32 15 C21 12 12 0.58000 0 3 16 17 18 16 O22 1 16 -0.38000 1 1 17 17 C22 15 4 0.00000 0 2 18 19 18 C23 15 4 0.00000 1 2 19 20 19 C24 15 4 0.00000 0 2 20 21 20 C25 15 4 0.00000 1 2 21 22 21 C26 15 4 0.00000 0 2 22 23 22 C27 15 4 0.00000 1 2 23 24 23 C28 15 4 0.00000 0 2 24 25 24 C29 15 4 0.00000 1 2 25 26 25 C210 15 4 0.00000 0 2 26 27 26 C211 15 4 0.00000 1 2 27 28 27 C212 15 4 0.00000 0 2 28 29 28 C213 15 4 0.00000 1 2 29 30 29 C214 15 4 0.00000 0 2 30 31 30 C215 15 4 0.00000 1 1 31 31 C216 16 5 0.00000 1 0 32 C1 15 4 0.16000 0 2 33 34 33 O11 4 16 -0.36000 0 3 34 35 36 34 C11 12 12 0.58000 0 3 35 36 37 35 O12 1 16 -0.38000 1 1 36 36 C12 15 4 0.00000 0 2 37 38 37 C13 15 4 0.00000 1 2 38 39 38 C14 15 4 0.00000 0 2 39 40 39 C15 15 4 0.00000 1 2 40 41 40 C16 15 4 0.00000 0 2 41 42 41 C17 15 4 0.00000 1 2 42 43 42 C18 15 4 0.00000 0 2 43 44 43 C19 15 4 0.00000 1 2 44 45 44 C110 15 4 0.00000 0 2 45 46 45 C111 15 4 0.00000 1 2 46 47 46 C112 15 4 0.00000 0 2 47 48 47 C113 15 4 0.00000 1 2 48 49 48 C114 15 4 0.00000 0 2 49 50 49 C115 15 4 0.00000 1 1 50 50 C116 16 5 0.00000 1 0 # bonds # NB 49 # IB JB MCB 1 4 21 2 4 21 3 4 21 4 5 21 5 6 27 6 7 18 7 8 28 8 9 24 8 10 24 8 11 28 11 12 18 12 13 27 13 14 18 13 32 27 14 15 10 15 16 5 15 17 23 17 18 27 18 19 27 19 20 27 20 21 27 21 22 27 22 23 27 23 24 27 24 25 27 25 26 27 26 27 27 27 28 27 28 29 27 29 30 27 30 31 27 32 33 18 33 34 10 34 35 5 34 36 23 36 37 27 37 38 27 38 39 27 39 40 27 40 41 27 41 42 27 42 43 27 43 44 27 44 45 27 45 46 27 46 47 27 47 48 27 48 49 27 49 50 27 # bond angles # NBA 57 # IB JB KB MCB 1 4 2 13 1 4 3 13 1 4 5 13 2 4 3 13 2 4 5 13 3 4 5 13 4 5 6 15 5 6 7 15 6 7 8 26 7 8 9 14 7 8 10 14 7 8 11 5 9 8 10 29 9 8 11 14 10 8 11 14 8 11 12 26 11 12 13 15 12 13 14 13 12 13 32 13 14 13 32 13 13 14 15 22 14 15 16 31 14 15 17 16 16 15 17 35 15 17 18 15 17 18 19 15 18 19 20 15 19 20 21 15 20 21 22 15 21 22 23 15 22 23 24 15 23 24 25 15 24 25 26 15 25 26 27 15 26 27 28 15 27 28 29 15 28 29 30 15 29 30 31 15 13 32 33 15 32 33 34 22 33 34 35 31 33 34 36 16 35 34 36 35 34 36 37 15 36 37 38 15 37 38 39 15 38 39 40 15 39 40 41 15 40 41 42 15 41 42 43 15 42 43 44 15 43 44 45 15 44 45 46 15 45 46 47 15 46 47 48 15 47 48 49 15 48 49 50 15 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 14 12 32 13 2 15 14 17 16 1 34 33 36 35 1 # dihedrals # NDA 43 # IB JB KB LB MCB 1 4 5 6 29 4 5 6 7 4 4 5 6 7 36 5 6 7 8 29 6 7 8 11 20 6 7 8 11 27 7 8 11 12 20 7 8 11 12 27 8 11 12 13 29 11 12 13 32 34 12 13 14 15 29 12 13 32 33 34 13 14 15 17 13 14 15 17 18 40 15 17 18 19 34 17 18 19 20 34 18 19 20 21 34 19 20 21 22 34 20 21 22 23 34 21 22 23 24 34 22 23 24 25 34 23 24 25 26 34 24 25 26 27 34 25 26 27 28 34 26 27 28 29 34 27 28 29 30 34 28 29 30 31 34 13 32 33 34 29 32 33 34 36 13 33 34 36 37 40 34 36 37 38 34 36 37 38 39 34 37 38 39 40 34 38 39 40 41 34 39 40 41 42 34 40 41 42 43 34 41 42 43 44 34 42 43 44 45 34 43 44 45 46 34 44 45 46 47 34 45 46 47 48 34 46 47 48 49 34 47 48 49 50 34 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE CH4 # building block (residue, nucleotide, etc.) # RNME CH4 # number of atoms, number of preceding exclusions # NMAT NLIN 1 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 CM 17 6 0.00000 1 0 # bonds # NB 0 # IB JB MCB # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE AR # building block (residue, nucleotide, etc.) # RNME AR # number of atoms, number of preceding exclusions # NMAT NLIN 1 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 AR 31 39 0.00000 1 0 # bonds # NB 0 # IB JB MCB # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 23 32 0.54000 0 4 2 3 4 5 2 IO1 2 16 -0.63500 0 3 3 4 5 3 IO2 2 16 -0.63500 0 2 4 5 4 IO3 2 16 -0.63500 0 1 5 5 IO4 2 16 -0.63500 1 0 # bonds # NB 4 # IB JB MCB 1 2 25 1 3 25 1 4 25 1 5 25 # bond angles # NBA 6 # IB JB KB MCB 2 1 3 13 2 1 4 13 2 1 5 13 3 1 4 13 3 1 5 13 4 1 5 13 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 27 65 2.00000 1 0 # bonds # NB 0 # IB JB MCB # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 37 23 1.00000 1 0 # bonds # NB 0 # IB JB MCB # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 38 35 -1.00000 1 0 # bonds # NB 0 # IB JB MCB # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 29 40 2.00000 1 0 # bonds # NB 0 # IB JB MCB # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 28 24 2.00000 1 0 # bonds # NB 0 # IB JB MCB # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE CU1+ # building block (residue, nucleotide, etc.) # RNME CU1+ # number of atoms, number of preceding exclusions # NMAT NLIN 1 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 CU 24 63 1.00000 1 0 # bonds # NB 0 # IB JB MCB # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE CU2+ # building block (residue, nucleotide, etc.) # RNME CU2+ # number of atoms, number of preceding exclusions # NMAT NLIN 1 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 CU 25 63 2.00000 1 0 # bonds # NB 0 # IB JB MCB # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 5 16 -0.82000 0 2 2 3 2 HW1 21 1 0.41000 0 1 3 3 HW2 21 1 0.41000 1 0 # bonds # NB 3 # IB JB MCB 1 2 38 1 3 38 2 3 46 # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 5 16 -0.84760 0 2 2 3 2 HW1 21 1 0.42380 0 1 3 3 HW2 21 1 0.42380 1 0 # bonds # NB 3 # IB JB MCB 1 2 38 1 3 38 2 3 46 # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 39 12 0.17900 0 4 2 3 4 5 2 HChl 41 1 0.08200 0 3 3 4 5 3 CLCh1 40 35 -0.08700 0 2 4 5 4 CLCh2 40 35 -0.08700 0 1 5 5 CLCh3 40 35 -0.08700 1 0 # bonds # NB 9 # IB JB MCB 1 3 40 1 4 40 1 5 40 2 3 47 2 4 47 2 5 47 3 4 48 3 5 48 4 5 48 # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 42 32 0.12753 0 3 2 3 4 2 ODmso 44 16 -0.44753 0 2 3 4 3 CDms1 43 5 0.16000 0 1 4 4 CDms2 43 5 0.16000 1 0 # bonds # NB 6 # IB JB MCB 1 2 41 1 3 42 1 4 42 2 3 49 2 4 49 3 4 50 # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 36 16 -0.67400 0 2 2 3 2 HMet 21 1 0.40800 0 1 3 3 CMet 35 5 0.26600 1 0 # bonds # NB 3 # IB JB MCB 1 2 1 1 3 27 2 3 51 # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.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 45 12 0.00000 0 4 2 3 4 5 2 CLCl1 46 35 0.00000 0 3 3 4 5 3 CLCl2 46 35 0.00000 0 2 4 5 4 CLCl3 46 35 0.00000 0 1 5 5 CLCl4 46 35 0.00000 1 0 # bonds # NB 9 # IB JB MCB 1 2 43 1 3 43 1 4 43 1 5 43 2 3 52 2 4 52 2 5 52 3 4 52 3 5 52 # bond angles # NBA 0 # IB JB KB MCB # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE TFE # building block (residue, nucleotide, etc.) # RNME TFE # number of atoms, number of preceding exclusions # NMAT NLIN 7 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 HT 21 1 0.41000 0 2 2 3 2 OT 50 16 -0.62500 0 2 3 4 3 CH2T 49 4 0.27300 0 4 4 5 6 7 4 CT 48 12 0.45200 0 3 5 6 7 5 F1T 47 19 -0.17000 0 2 6 7 6 F2T 47 19 -0.17000 0 1 7 7 F3T 47 19 -0.17000 1 0 # bonds # NB 6 # IB JB MCB 1 2 1 2 3 18 3 4 27 4 5 13 4 6 13 4 7 13 # bond angles # NBA 8 # IB JB KB MCB 1 2 3 50 2 3 4 51 3 4 5 52 3 4 6 52 3 4 7 52 5 4 6 49 5 4 7 49 6 4 7 49 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 1 2 3 4 24 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb53a6.dat SOL TYPE UREA # building block (residue, nucleotide, etc.) # RNME UREA # number of atoms, number of preceding exclusions # NMAT NLIN 8 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 OU 52 16 -0.39000 0 7 2 3 4 5 6 7 8 2 CU 51 12 0.14200 0 6 3 4 5 6 7 8 3 N1U 53 14 -0.54200 0 5 4 5 6 7 8 4 H11U 21 1 0.33300 0 4 5 6 7 8 5 H12U 21 1 0.33300 0 3 6 7 8 6 N2U 53 14 -0.54200 0 2 7 8 7 H21U 21 1 0.33300 0 1 8 8 H22U 21 1 0.33300 1 0 # bonds # NB 7 # IB JB MCB 1 2 44 2 3 45 2 6 45 3 4 2 3 5 2 6 7 2 6 8 2 # bond angles # NBA 9 # IB JB KB MCB 1 2 3 54 1 2 6 54 3 2 6 53 2 3 4 23 2 3 5 23 4 3 5 24 2 6 7 23 2 6 8 23 7 6 8 24 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 2 3 6 1 1 3 4 5 2 1 6 7 8 2 1 # dihedrals # NDA 2 # IB JB KB LB MCB 1 2 3 4 15 1 2 6 7 15 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE mtb53a6.dat SVT TYPE H2O #solvent name #RNMES H2O #number of atoms 3 #atoms #ATOM ANM IAC MASS CG 1 OW 5 16 -.82 2 HW1 21 1 .41 3 HW2 21 1 .41 #constraints #number 3 # IB JB LENGTH 1 2 0.1 1 3 0.1 2 3 0.163299 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE mtb53a6.dat SVT TYPE H2OE #solvent name #RNMES H2OE #number of atoms 3 #atoms #ATOM ANM IAC MASS CG 1 OW 5 16 -.8476 2 HW1 21 1 .4238 3 HW2 21 1 .4238 #constraints #number 3 # IB JB LENGTH 1 2 0.1 1 3 0.1 2 3 0.163299 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE mtb53a6.dat SVT TYPE CHCL3 #solvent name #RNMES CHCL3 #number of atoms 5 #atoms #ATOM ANM IAC MASS CG 1 CChl 39 12 .179 2 HChl 41 1 .082 3 CLCh1 40 35 -.087 4 CLCh2 40 35 -.087 5 CLCh3 40 35 -.087 #constraints #number 9 # IB JB LENGTH 1 3 0.1758 1 4 0.1758 1 5 0.1758 2 3 0.233839 2 4 0.233839 2 5 0.233839 3 4 0.290283 3 5 0.290283 4 5 0.290283 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE mtb53a6.dat SVT TYPE DMSO #solvent name #RNMES DMSO #number of atoms 4 #atoms #ATOM ANM IAC MASS CG 1 SDmso 42 32 .12753 2 ODmso 44 16 -.44753 3 CDms1 43 5 .16 4 CDms2 43 5 .16 #constraints #number 6 # IB JB LENGTH 1 2 0.153 1 3 0.1937991 1 4 0.1937991 2 3 0.2793883 2 4 0.2793883 3 4 0.2911886 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE mtb53a6.dat SVT TYPE CH3OH #solvent name #RNMES CH3OH #number of atoms 3 #atoms #ATOM ANM IAC MASS CG 1 OMet 36 16 -.674 2 HMet 21 1 .408 3 CMet 35 5 .266 #constraints #number 3 # IB JB LENGTH 1 2 0.1000 1 3 0.1530 2 3 0.2077 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE mtb53a6.dat SVT TYPE CCL4 #solvent name #RNMES CCL4 #number of atoms 5 #atoms #ATOM ANM IAC MASS CG 1 CCl4 45 12 .0 2 CLCl1 46 35 .0 3 CLCl2 46 35 .0 4 CLCl3 46 35 .0 5 CLCl4 46 35 .0 #constraints #number 9 # IB JB LENGTH 1 2 0.176 1 3 0.176 1 4 0.176 1 5 0.176 2 3 0.287407 2 4 0.287407 2 5 0.287407 3 4 0.287407 3 5 0.287407 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE mtb53a6.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 21 1 0.24800 0 4 2 3 4 5 2 H2 21 1 0.24800 0 3 3 4 5 # replacing atoms 3 N 8 14 0.12900 0 4 H3 21 1 0.24800 0 5 CA 14 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 10 1 3 4 10 1 3 5 11 2 3 4 10 2 3 5 11 4 3 5 11 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 2 3 5 6 29 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE mtb53a6.dat INI TYPE NH2 # building block (residue, nucleotide, etc.) # RNME NH2 # number of atoms, number of atoms to be replaced # NMAT NREP 4 3 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H1 21 1 0.44000 0 3 2 3 4 # replacing atoms 2 N 7 14 -0.64000 0 3 H2 21 1 0.44000 0 4 CA 14 3 -0.24000 1 # bonds # NB 1 # IB JB MCB 1 2 2 # bond angles # NBA 3 # IB JB KB MCB 1 2 3 10 1 2 4 11 3 2 4 11 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 1 2 4 5 29 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE mtb53a6.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 21 1 0.24800 0 4 2 3 4 7 2 H2 21 1 0.24800 0 3 3 4 7 # replacing atoms 3 N 8 14 0.12800 0 4 CA 14 3 0.18800 0 5 CB 15 4 0.00000 0 6 CG 15 4 0.00000 0 7 CD 15 4 0.18800 1 # bonds # NB 7 # IB JB MCB 1 3 2 2 3 2 3 4 21 3 7 21 4 5 27 5 6 27 6 7 27 # bond angles # NBA 10 # IB JB KB MCB 1 3 2 10 1 3 4 11 1 3 7 11 2 3 4 11 2 3 7 11 4 3 7 21 3 4 5 13 4 5 6 13 5 6 7 13 3 7 6 13 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 2 3 4 8 29 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE mtb53a6.dat TER TYPE COO- # building block (residue, nucleotide, etc.) # RNME COO- # number of atoms, number of atoms to be replaced # NMAT NREP 3 -2 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C 12 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 6 1 3 6 # bond angles # NBA 3 # IB JB KB MCB 0 1 2 22 0 1 3 22 2 1 3 38 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB #@FREELINE END MTBUILDBLEND #@BLOCKTYPE mtb53a6.dat TER TYPE COOH # building block (residue, nucleotide, etc.) # RNME COOH # number of atoms, number of atoms to be replaced # NMAT NREP 4 -2 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C 12 12 0.33000 0 3 2 3 4 2 O1 1 16 -0.45000 0 1 3 3 O2 3 16 -0.28800 0 1 4 4 H 21 1 0.40800 1 0 # bonds # NB 3 # IB JB MCB 1 2 5 1 3 13 3 4 1 # bond angles # NBA 1 # IB JB KB MCB 1 3 4 12 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 0 1 3 4 12 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE mtb53a6.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 # replacing atoms 1 H5* 21 1 0.39800 0 2 O1P 0 1 0.00000 0 3 O2P 0 1 0.00000 0 4 O5* 3 16 -0.54800 0 5 C5* 15 4 0.15000 1 # bonds # NB 2 # IB JB MCB 1 4 1 4 5 20 # bond angles # NBA 1 # IB JB KB MCB 1 4 5 12 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 1 4 5 6 23 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE mtb53a6.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 # replacing atoms 1 H5* 21 1 0.39800 0 2 O1P 0 1 0.00000 0 3 O2P 0 1 0.00000 0 4 O5* 3 16 -0.54800 0 5 C5* 15 4 0.15000 1 # bonds # NB 2 # IB JB MCB 1 4 1 4 5 20 # bond angles # NBA 1 # IB JB KB MCB 1 4 5 12 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 1 4 5 6 23 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE mtb53a6.dat TER TYPE D3OH # building block (residue, nucleotide, etc.) # RNME D3OH # number of atoms, number of atoms to be replaced # NMAT NREP 4 -3 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C2* 18 4 0.00000 1 2 2 3 2 C3* 14 3 0.15000 0 2 3 4 3 O3* 3 16 -0.54800 0 1 4 4 H3* 21 1 0.39800 1 0 # bonds # NB 2 # IB JB MCB 2 3 20 3 4 1 # bond angles # NBA 1 # IB JB KB MCB 2 3 4 12 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 0 2 3 4 23 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE mtb53a6.dat TER TYPE 3OH # building block (residue, nucleotide, etc.) # RNME 3OH # number of atoms, number of atoms to be replaced # NMAT NREP 6 -5 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C2* 14 3 0.15000 0 4 2 3 4 5 2 O2* 3 16 -0.54800 0 2 3 4 3 H2* 21 1 0.39800 1 0 4 C3* 14 3 0.15000 0 2 5 6 5 O3* 3 16 -0.54800 0 1 6 6 H3* 21 1 0.39800 1 0 # bonds # NB 5 # IB JB MCB 1 2 20 1 4 26 2 3 1 4 5 20 5 6 1 # bond angles # NBA 4 # IB JB KB MCB 2 1 4 9 1 2 3 12 1 4 5 9 4 5 6 12 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 1 # IB JB KB LB MCB 0 4 5 6 29 #@FREELINE END