TITLE File : 54a7.mtb Force field : 54A7 (condensed-phase simulations) Reference : Schmid et al. Eur. Biophys. J. 2011, in press File content : molecular topology building blocks (alpha amino acids, nucleic acids, lipids) Format : GROMOS11 Initial file : WFVG, AM, CO, JD Zuerich, Sep. 2010 Time stamp : PHH, Thu Nov 10 22:17:15 CET 2011 Remark : Change from 53A(B)6 involves peptide phi/psi torsions, choline CH3 atom type, and new vDW parameters for Na+ and Cl-; AIB bulding block added 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, 15.09.2011: Corrected the phi/psi dihedral potentials for residue AIB in the G96 and G11 54A7 and 54B7 mtb files (they had not been updated from 53A(B)6; found by Alpesh Malde) PHH, 15.09.2011: Corrected the atom charges for residue DPPC in the G96 and G11 54A7 mtb files (they had not been updated from 53A6; found by Alpesh Malde). Note that the DPPC charges in 54B7 are kept the same as in 53B6, i.e. not updated (they differ between 53A6 and 53B6, and an update scheme is neither obvious nor really urgent). PHH, 09.11.2011: Reintroduced a FORCEFIELD block in all GROMOS11 files. 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 54A7 END PHYSICALCONSTANTS # FPEPSI: 1.0/(4.0*PI*EPS0) (EPS0 is the permittivity of vacuum) 0.1389354E+03 # HBAR: Planck's constant HBAR = H/(2* PI) 0.6350780E-01 # SPDL: Speed of light (in nm/ps) 2.9979245800E05 # BOLTZ: Boltzmann's constant 8.31441E-03 END LINKEXCLUSIONS #nearest neighbour exclusions when linking #NRNE 2 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 5 44 -1 1 3 5 43 1 3 5 7 45 1 3 5 7 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 12 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 16 44 -1 1 3 16 43 1 3 4 5 34 1 3 16 18 45 1 3 16 18 42 3 4 5 6 34 4 5 6 7 34 5 6 7 9 39 6 7 9 10 14 7 9 10 11 14 7 9 13 14 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 12 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 15 44 -1 1 3 15 43 1 3 4 5 34 1 3 15 17 45 1 3 15 17 42 3 4 5 6 34 4 5 6 7 34 5 6 7 9 39 6 7 9 10 14 7 9 10 11 14 7 9 12 13 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 8 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 10 44 -1 1 3 10 43 1 3 4 5 34 1 3 10 12 45 1 3 10 12 42 3 4 5 7 40 4 5 7 8 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 8 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 10 44 -1 1 3 10 43 1 3 4 5 34 1 3 10 12 45 1 3 10 12 42 3 4 5 7 40 4 5 7 8 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 44 -1 1 3 8 43 1 3 4 5 34 1 3 8 10 45 1 3 8 10 42 3 4 5 6 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 8 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 9 44 -1 1 3 9 43 1 3 4 5 34 1 3 9 11 45 1 3 9 11 42 3 4 5 7 40 4 5 7 8 12 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 6 44 -1 1 3 6 43 1 3 4 5 34 1 3 6 8 45 1 3 6 8 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 44 -1 1 3 7 43 1 3 4 5 34 1 3 7 9 45 1 3 7 9 42 3 4 5 6 26 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 9 # IB JB KB LB MCB 5 -5 -4 -3 26 -4 -5 5 4 21 -2 -1 1 3 14 -1 1 3 6 44 -1 1 3 6 43 1 3 4 5 34 1 3 6 8 45 1 3 6 8 42 3 4 5 -5 26 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 6 44 -1 1 3 6 43 1 3 4 5 34 1 3 6 8 45 1 3 6 8 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 9 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 11 44 -1 1 3 11 43 1 3 4 5 34 1 3 11 13 45 1 3 11 13 42 3 4 5 6 34 4 5 6 8 40 5 6 8 9 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 8 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 9 44 -1 1 3 9 43 1 3 4 5 34 1 3 9 11 45 1 3 9 11 42 3 4 5 6 34 4 5 6 8 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 9 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 10 44 -1 1 3 10 43 1 3 4 5 34 1 3 10 12 45 1 3 10 12 42 3 4 5 6 34 4 5 6 8 40 5 6 8 9 12 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 4 44 -1 1 3 4 43 1 3 4 6 45 1 3 4 6 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 13 44 -1 1 3 13 43 1 3 4 5 34 1 3 13 15 45 1 3 13 15 42 3 4 5 6 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 13 44 -1 1 3 13 43 1 3 4 5 34 1 3 13 15 45 1 3 13 15 42 3 4 5 6 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 14 44 -1 1 3 14 43 1 3 4 5 34 1 3 14 16 45 1 3 14 16 42 3 4 5 6 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 8 # IB JB KB LB MCB -2 -1 1 3 14 -2 -1 12 8 38 -1 1 3 13 44 -1 1 3 13 43 1 3 4 5 34 1 3 13 15 45 1 3 13 15 42 3 4 5 6 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 8 # IB JB KB LB MCB -2 -1 1 3 14 -2 -1 12 8 38 -1 1 3 13 44 -1 1 3 13 43 1 3 4 5 34 1 3 13 15 45 1 3 13 15 42 3 4 5 6 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 10 # IB JB KB LB MCB -2 -1 1 2 14 -1 1 2 8 44 -1 1 2 8 43 2 1 7 4 39 1 2 3 4 34 1 2 8 10 45 1 2 8 10 42 2 3 4 7 34 3 4 5 6 23 3 4 7 1 34 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 44 -1 1 3 8 43 1 3 4 5 34 1 3 8 10 45 1 3 8 10 42 3 4 5 7 34 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 44 -1 1 3 8 43 1 3 4 5 34 1 3 8 10 45 1 3 8 10 42 3 4 5 6 34 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 10 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 11 44 -1 1 3 11 43 1 3 4 5 34 1 3 11 13 45 1 3 11 13 42 3 4 5 6 34 4 5 6 7 34 5 6 7 8 34 6 7 8 9 29 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 10 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 12 44 -1 1 3 12 43 1 3 4 5 34 1 3 12 14 45 1 3 12 14 42 3 4 5 6 34 4 5 6 7 34 5 6 7 8 34 6 7 8 9 29 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 8 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 44 -1 1 3 8 43 1 3 4 5 34 1 3 8 10 45 1 3 8 10 42 3 4 5 6 34 4 5 6 7 26 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 16 44 -1 1 3 16 43 1 3 4 5 34 1 3 16 18 45 1 3 16 18 42 3 4 5 6 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 9 # IB JB KB LB MCB -2 -1 1 2 14 -1 1 2 6 44 -1 1 2 6 43 2 1 5 4 39 1 2 3 4 34 1 2 6 8 45 1 2 6 8 42 2 3 4 5 34 3 4 5 1 34 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 44 -1 1 3 7 43 1 3 4 5 34 1 3 7 9 45 1 3 7 9 42 3 4 5 6 23 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 44 -1 1 3 8 43 1 3 4 5 34 1 3 8 10 45 1 3 8 10 42 3 4 5 6 23 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 20 44 -1 1 3 20 43 1 3 4 5 34 1 3 20 22 45 1 3 20 22 42 3 4 5 8 40 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 8 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 17 44 -1 1 3 17 43 1 3 4 5 34 1 3 17 19 45 1 3 17 19 42 3 4 5 6 40 10 14 15 16 11 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 44 -1 1 3 7 43 1 3 4 5 34 1 3 7 9 45 1 3 7 9 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 5 44 -1 1 3 5 43 1 3 5 7 45 1 3 5 7 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 6 44 -1 1 3 6 43 1 3 4 5 34 1 3 6 8 45 1 3 6 8 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.dat SOL TYPE AIB # building block (residue, nucleotide, etc.) # RNME AIB # number of atoms, number of preceding exclusions # NMAT NLIN 7 2 # preceding exclusions #ATOM MAE MSAE -1 4 0 1 2 3 0 1 1 # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 N 6 14 -0.31000 0 5 2 3 4 5 6 2 H 21 1 0.31000 1 1 3 3 CA 14 3 0.00000 0 5 4 5 6 7 8 4 CB 16 5 0.00000 0 2 5 6 5 CG 16 5 0.00000 1 1 6 # trailing atoms #ATOM ANM IACM MASS CGMICGM 6 C 12 12 0.45000 0 7 O 1 16 -0.45000 1 # bonds # NB 7 # IB JB MCB 1 2 2 1 3 21 3 4 27 3 5 27 3 6 27 6 7 5 6 8 10 # bond angles # NBA 12 # IB JB KB MCB -1 1 2 32 -1 1 3 31 2 1 3 18 1 3 4 13 1 3 5 13 1 3 6 13 4 3 5 13 4 3 6 13 5 3 6 13 3 6 7 30 3 6 8 19 7 6 8 33 # improper dihedrals # NIDA 2 # IB JB KB LB MCB 1 -1 3 2 1 6 3 8 7 1 # dihedrals # NDA 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 6 44 -1 1 3 6 43 1 3 6 8 45 1 3 6 8 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 11 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 13 44 -1 1 3 13 43 1 3 4 7 34 1 3 13 15 45 1 3 13 15 42 3 4 5 6 23 3 4 7 9 34 4 7 9 10 34 7 9 10 11 40 9 10 11 12 14 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 7 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 8 44 -1 1 3 8 43 1 3 4 5 34 1 3 8 10 45 1 3 8 10 42 3 4 5 6 34 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 6 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 7 44 -1 1 3 7 43 1 3 4 5 34 1 3 7 9 45 1 3 7 9 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 5 # IB JB KB LB MCB -2 -1 1 3 14 -1 1 3 4 44 -1 1 3 4 43 1 3 4 6 45 1 3 4 6 42 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 54 5 0.40000 0 4 2 3 4 5 2 C34 54 5 0.40000 0 3 3 4 5 3 C35 54 5 0.40000 0 2 4 5 4 N 8 14 -0.50000 0 2 5 6 5 C32 15 4 0.30000 1 2 6 7 6 C31 15 4 0.40000 0 2 7 8 7 O32 3 16 -0.80000 0 4 8 9 10 11 8 P 30 31 1.70000 0 4 9 10 11 12 9 O33 2 16 -0.80000 0 2 10 11 10 O34 2 16 -0.80000 0 1 11 11 O31 3 16 -0.70000 1 2 12 13 12 C3 15 4 0.40000 0 3 13 14 32 13 C2 14 3 0.30000 0 4 14 15 32 33 14 O21 4 16 -0.70000 0 4 15 16 17 32 15 C21 12 12 0.70000 0 3 16 17 18 16 O22 1 16 -0.70000 1 1 17 17 C22 15 4 0.00000 1 2 18 19 18 C23 15 4 0.00000 1 2 19 20 19 C24 15 4 0.00000 1 2 20 21 20 C25 15 4 0.00000 1 2 21 22 21 C26 15 4 0.00000 1 2 22 23 22 C27 15 4 0.00000 1 2 23 24 23 C28 15 4 0.00000 1 2 24 25 24 C29 15 4 0.00000 1 2 25 26 25 C210 15 4 0.00000 1 2 26 27 26 C211 15 4 0.00000 1 2 27 28 27 C212 15 4 0.00000 1 2 28 29 28 C213 15 4 0.00000 1 2 29 30 29 C214 15 4 0.00000 1 2 30 31 30 C215 15 4 0.00000 1 1 31 31 C216 16 5 0.00000 1 0 32 C1 15 4 0.50000 0 2 33 34 33 O11 4 16 -0.70000 0 3 34 35 36 34 C11 12 12 0.80000 0 3 35 36 37 35 O12 1 16 -0.60000 1 1 36 36 C12 15 4 0.00000 1 2 37 38 37 C13 15 4 0.00000 1 2 38 39 38 C14 15 4 0.00000 1 2 39 40 39 C15 15 4 0.00000 1 2 40 41 40 C16 15 4 0.00000 1 2 41 42 41 C17 15 4 0.00000 1 2 42 43 42 C18 15 4 0.00000 1 2 43 44 43 C19 15 4 0.00000 1 2 44 45 44 C110 15 4 0.00000 1 2 45 46 45 C111 15 4 0.00000 1 2 46 47 46 C112 15 4 0.00000 1 2 47 48 47 C113 15 4 0.00000 1 2 48 49 48 C114 15 4 0.00000 1 2 49 50 49 C115 15 4 0.00000 1 1 50 50 C116 16 5 0.00000 1 0 # bonds # NB 49 # IB JB MCB 1 4 21 2 4 21 3 4 21 4 5 21 5 6 27 6 7 18 7 8 28 8 9 24 8 10 24 8 11 28 11 12 18 12 13 27 13 14 18 13 32 27 14 15 10 15 16 5 15 17 23 17 18 27 18 19 27 19 20 27 20 21 27 21 22 27 22 23 27 23 24 27 24 25 27 25 26 27 26 27 27 27 28 27 28 29 27 29 30 27 30 31 27 32 33 18 33 34 10 34 35 5 34 36 23 36 37 27 37 38 27 38 39 27 39 40 27 40 41 27 41 42 27 42 43 27 43 44 27 44 45 27 45 46 27 46 47 27 47 48 27 48 49 27 49 50 27 # bond angles # NBA 57 # IB JB KB MCB 1 4 2 13 1 4 3 13 1 4 5 13 2 4 3 13 2 4 5 13 3 4 5 13 4 5 6 15 5 6 7 15 6 7 8 26 7 8 9 14 7 8 10 14 7 8 11 5 9 8 10 29 9 8 11 14 10 8 11 14 8 11 12 26 11 12 13 15 12 13 14 13 12 13 32 13 14 13 32 13 13 14 15 22 14 15 16 31 14 15 17 16 16 15 17 35 15 17 18 15 17 18 19 15 18 19 20 15 19 20 21 15 20 21 22 15 21 22 23 15 22 23 24 15 23 24 25 15 24 25 26 15 25 26 27 15 26 27 28 15 27 28 29 15 28 29 30 15 29 30 31 15 13 32 33 15 32 33 34 22 33 34 35 31 33 34 36 16 35 34 36 35 34 36 37 15 36 37 38 15 37 38 39 15 38 39 40 15 39 40 41 15 40 41 42 15 41 42 43 15 42 43 44 15 43 44 45 15 44 45 46 15 45 46 47 15 46 47 48 15 47 48 49 15 48 49 50 15 # improper dihedrals # NIDA 3 # IB JB KB LB MCB 14 12 32 13 2 15 14 17 16 1 34 33 36 35 1 # dihedrals # NDA 43 # IB JB KB LB MCB 1 4 5 6 29 4 5 6 7 4 4 5 6 7 36 5 6 7 8 29 6 7 8 11 20 6 7 8 11 27 7 8 11 12 20 7 8 11 12 27 8 11 12 13 29 11 12 13 32 34 12 13 14 15 29 12 13 32 33 34 13 14 15 17 13 14 15 17 18 40 15 17 18 19 34 17 18 19 20 34 18 19 20 21 34 19 20 21 22 34 20 21 22 23 34 21 22 23 24 34 22 23 24 25 34 23 24 25 26 34 24 25 26 27 34 25 26 27 28 34 26 27 28 29 34 27 28 29 30 34 28 29 30 31 34 13 32 33 34 29 32 33 34 36 13 33 34 36 37 40 34 36 37 38 34 36 37 38 39 34 37 38 39 40 34 38 39 40 41 34 39 40 41 42 34 40 41 42 43 34 41 42 43 44 34 42 43 44 45 34 43 44 45 46 34 44 45 46 47 34 45 46 47 48 34 46 47 48 49 34 47 48 49 50 34 #@FREELINE # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLUTE #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLSOLVENT #@BLOCKTYPE mtb54a7.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 mtb54a7.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 mtb54a7.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 mtb54a7.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 mtb54a7.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 mtb54a7.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 mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END MTBUILDBLEND #@BLOCKTYPE mtb54a7.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 # LJ exceptions # NEX 0 END