packmol-memgen-minimal 1.1.16__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- packmol_memgen/__init__.py +2 -0
- packmol_memgen/__version__.py +34 -0
- packmol_memgen/data/LICENSE.Apache-2.0 +201 -0
- packmol_memgen/data/extra_solvents.lib +789 -0
- packmol_memgen/data/frcmod.lipid_ext +97 -0
- packmol_memgen/data/frcmod.solvents +129 -0
- packmol_memgen/data/insane_lipids.txt +138 -0
- packmol_memgen/data/insane_solvents.txt +45 -0
- packmol_memgen/data/leaprc.extra_solvents +42 -0
- packmol_memgen/data/leaprc.lipid_ext +48 -0
- packmol_memgen/data/lipid_ext.lib +12312 -0
- packmol_memgen/data/martini_v3.0.0.itp +356605 -0
- packmol_memgen/data/memgen.parm +4082 -0
- packmol_memgen/data/pdbs.tar.gz +0 -0
- packmol_memgen/data/solvent.parm +14 -0
- packmol_memgen/example/example.sh +31 -0
- packmol_memgen/lib/__init__.py +0 -0
- packmol_memgen/lib/amber.py +77 -0
- packmol_memgen/lib/charmmlipid2amber/__init__.py +0 -0
- packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.csv +7164 -0
- packmol_memgen/lib/charmmlipid2amber/charmmlipid2amber.py +225 -0
- packmol_memgen/lib/pdbremix/LICENSE +21 -0
- packmol_memgen/lib/pdbremix/__init__.py +0 -0
- packmol_memgen/lib/pdbremix/_version.py +1 -0
- packmol_memgen/lib/pdbremix/amber.py +1103 -0
- packmol_memgen/lib/pdbremix/asa.py +227 -0
- packmol_memgen/lib/pdbremix/data/aminoacid.pdb +334 -0
- packmol_memgen/lib/pdbremix/data/binaries.json +26 -0
- packmol_memgen/lib/pdbremix/data/charmm22.parameter +2250 -0
- packmol_memgen/lib/pdbremix/data/charmm22.topology +1635 -0
- packmol_memgen/lib/pdbremix/data/color_b.py +682 -0
- packmol_memgen/lib/pdbremix/data/hin.lib +130 -0
- packmol_memgen/lib/pdbremix/data/hydroxide.lib +88 -0
- packmol_memgen/lib/pdbremix/data/make_chi.py +92 -0
- packmol_memgen/lib/pdbremix/data/opls.parameter +1108 -0
- packmol_memgen/lib/pdbremix/data/opls.topology +1869 -0
- packmol_memgen/lib/pdbremix/data/phd.frcmod +82 -0
- packmol_memgen/lib/pdbremix/data/phd.leaprc +4 -0
- packmol_memgen/lib/pdbremix/data/phd.prepin +35 -0
- packmol_memgen/lib/pdbremix/data/template.pdb +334 -0
- packmol_memgen/lib/pdbremix/data/znb.frcmod +24 -0
- packmol_memgen/lib/pdbremix/data/znb.leaprc +7 -0
- packmol_memgen/lib/pdbremix/data/znb.lib +69 -0
- packmol_memgen/lib/pdbremix/data.py +264 -0
- packmol_memgen/lib/pdbremix/fetch.py +102 -0
- packmol_memgen/lib/pdbremix/force.py +627 -0
- packmol_memgen/lib/pdbremix/gromacs.py +978 -0
- packmol_memgen/lib/pdbremix/lib/__init__.py +0 -0
- packmol_memgen/lib/pdbremix/lib/docopt.py +579 -0
- packmol_memgen/lib/pdbremix/lib/pyqcprot.py +305 -0
- packmol_memgen/lib/pdbremix/namd.py +1078 -0
- packmol_memgen/lib/pdbremix/pdbatoms.py +543 -0
- packmol_memgen/lib/pdbremix/pdbtext.py +120 -0
- packmol_memgen/lib/pdbremix/protein.py +311 -0
- packmol_memgen/lib/pdbremix/pymol.py +480 -0
- packmol_memgen/lib/pdbremix/rmsd.py +203 -0
- packmol_memgen/lib/pdbremix/simulate.py +420 -0
- packmol_memgen/lib/pdbremix/spacehash.py +73 -0
- packmol_memgen/lib/pdbremix/trajectory.py +286 -0
- packmol_memgen/lib/pdbremix/util.py +273 -0
- packmol_memgen/lib/pdbremix/v3.py +16 -0
- packmol_memgen/lib/pdbremix/v3array.py +482 -0
- packmol_memgen/lib/pdbremix/v3numpy.py +350 -0
- packmol_memgen/lib/pdbremix/volume.py +155 -0
- packmol_memgen/lib/utils.py +1017 -0
- packmol_memgen/main.py +2827 -0
- packmol_memgen_minimal-1.1.16.dist-info/METADATA +664 -0
- packmol_memgen_minimal-1.1.16.dist-info/RECORD +71 -0
- packmol_memgen_minimal-1.1.16.dist-info/WHEEL +4 -0
- packmol_memgen_minimal-1.1.16.dist-info/entry_points.txt +2 -0
- packmol_memgen_minimal-1.1.16.dist-info/licenses/LICENSE +338 -0
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remarks 08-26-96
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remarks X-PLOR TOPOLOGY FILE FOR OPLS FORCE FIELD
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remarks OPLS NONBONDED AND TORSIONAL PARMS USED WITH AMBER BONDED AND VALENCE
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remarks PARMS
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remarks ATOM TYPES COMPATIBLE WITH AMBER TYPES
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remarks UNITED-ATOM REPRESENTATION for ALIPHATIC RESIDUES
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remarks ALL-ATOM REPRESENTATION for AROMATIC RESIDUES
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set echo=false end
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set message=off end
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! LOCAL ACCESS - UNDER CONSTRUCTION
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! Proteins only - DNA Bases to Follow
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! INCLUDED FLEXIBLE SOLVENTS: TIP3P, Urea, TFE(AA) - Others to Follow
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! INCLUDED COUNTERIONS: Na+, Cl-, NH4+, (SO4)2- - Others to Follow
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! Ca+2 and Yb+3 INCLUDED FOR CA-BINDING PROTEINS
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! USEFUL REFERENCES:
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! JACS, 1988, 110, 1657-1666
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! JACS, 1990, 112, 4768-4774
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! JACS, 1991, 113, 2810-2819
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! JPC , 1983, 79, 926 - 935
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! IsrJC, 1993, 33, 323 - 330
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! JACS, 1984, 106, 903 - 910
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! JPC , 1990, 94, 8021-8024
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! JPC , 1986, 90, 2174-2182
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! JPC , 1994, 98, 6225-6230
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! SMALL ALPHABETICAL CHARACTERS ATTACHED TO A STANDARD
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! AMBER ATOM TYPE (e.g., C3,C3a,C3b...) INDICATE A
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! DIFFERENCE IN L-J PARAMETERS WITHIN THE GENERAL TYPE
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! OR DISTINGUISH AMONG TYPES FOR TORSIONAL PARAMETERS
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autogenerate angles=true end
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! ========== MASS ASSIGNMENTS ==========
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MASS H 1.0079 ! amide and imino hydrogen - mainly backbone
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MASS Ha 1.0079 ! specific to urea and C-terminal amino cap
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MASS Hb 1.0079 ! specific to ASN and GLN
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MASS H3 1.0079 ! positively-charged hydrogen (ammonium ion)
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MASS HC 1.0079 ! hydrogen EXPLICITLY attached to carbon (aromatic)
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MASS HCa 1.0079 ! hydrogen EXPLICITLY attached to carbon (aliphatic)
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MASS HO 1.0079 ! hydroxyl hydrogen
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MASS HS 1.0079 ! thiol hydrogen
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MASS HW 1.0079 ! TIP3P water hydrogen
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MASS C 12.011 ! sp2 carbonyl carbon
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MASS C1 12.011 ! sp2 carbonyl carbon specific to urea
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MASS CAb 12.011 ! sp2 all-atom substituted aromatic carbon
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MASS C2 14.0268 ! sp3 aliphatic carbon with 2 implicit hydrogens
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MASS C2a 14.0268 ! sp3 aliphatic carbon with 2 implicit hydrogens
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MASS C2p 14.0268 ! sp3 aliphatic carbon with 2 implicit hydrogens
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! ( here, specific to proline and hydroxyproline)
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MASS C3 15.0347 ! sp3 aliphatic carbon with 3 implicit hydrogens
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MASS C3a 15.0347 ! sp3 aliphatic carbon with 3 implicit hydrogens
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MASS C3b 15.0347 ! sp3 aliphatic carbon with 3 implicit hydrogens
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MASS C3c 15.0347 ! sp3 aliphatic carbon with 3 implicit hydrogens
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MASS CA 12.011 ! sp2 all-atom benzenoid carbon
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MASS CAa 12.011 ! sp2 guanidino carbon
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MASS CB 12.011 ! sp2 all-atom aromatic fusion carbon
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MASS CC 12.011 ! sp2 all-atom pyrrole carbon (adjacent to N)
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MASS CH 13.0189 ! sp3 aliphatic carbon with 1 implicit hydrogen
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MASS CHa 13.0189 ! sp3 aliphatic carbon with 1 implicit hydrogen
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MASS CHp 13.0189 ! sp3 aliphatic carbon with 1 implicit hydrogen
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! ( here, specific to proline and hydroxyproline)
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MASS C0 12.011 ! sp3 tertiary carbon
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MASS CT 12.011 ! sp3 all-atom aliphatic carbon
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! ( here, CT = AMBER all-atom sp3 carbon)
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MASS CTf 12.011 ! sp3 all-atom fluorinated carbon
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! ( here, CT = AMBER all-atom sp3 carbon)
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MASS N 14.0067 ! pyramidal (sp2) amide nitrogen
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MASS N2 14.0067 ! guanidino nitrogen
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MASS N3 14.0067 ! ammonium-like nitrogen (sp3)
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MASS NA 14.0067 ! pyrrole (imidazole) or indole nitrogen
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! (H to be attached)
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MASS NB 14.0067 ! imidazole nitrogen with sp2-sp2 bonds (no H)
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MASS O 15.9994 ! carbonyl oxygen
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MASS O2 15.9994 ! carboxyl oxygen (LPs implicit)
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MASS O4 15.9994 ! sulfate oxygen (LPs implicit)
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MASS OH 15.9994 ! alcohol oxygen
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MASS OS 15.9994 ! ether (ester) oxygen
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MASS OW 15.9994 ! TIP3P water oxygen
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MASS S 32.06 ! sulfide (-ate) sulfur
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MASS SH 32.06 ! thiol sulfur
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MASS F 18.9984 ! fluoride substituent
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MASS SOD 22.9898 ! sodium +1 cation
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MASS CAL 40.08 ! calcium +2 cation
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MASS CHL 35.453 ! chloride -1 anion
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MASS YB 173.04 ! ytterbium +3 cation
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! ========== END MASS ASSIGNMENTS ==========
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! ========== RESIDUE CONSTRUCTION ==========
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! ========== UNCAPPED AAs ==========
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! ==GLY==
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RESIdue GLY
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GROUp
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ATOM N TYPE= N CHARge= -0.570 END
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ATOM H TYPE= H CHARge= 0.370 END
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ATOM CA TYPE= C2 CHARge= 0.200 END
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ATOM C TYPE= C CHARge= 0.500 END
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ATOM O TYPE= O CHARge= -0.500 END
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BOND H N BOND CA N BOND C CA BOND O C
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DIHEdral C CA N H
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DIHEdral O C CA N
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END
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! ==GLY==
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! ==ALA==
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RESIdue ALA
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GROUp
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ATOM N TYPE= N CHARge= -0.570 END
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ATOM H TYPE= H CHARge= 0.370 END
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ATOM CA TYPE= CH CHARge= 0.200 END
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ATOM C TYPE= C CHARge= 0.500 END
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ATOM O TYPE= O CHARge= -0.500 END
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ATOM CB TYPE= C3 CHARge= 0.000 END
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BOND H N BOND CA N BOND C CA BOND O C
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BOND CB CA
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DIHEdral C CA N H
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DIHEdral O C CA N
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DIHEdral CB CA N H
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DIHEdral CB CA C O
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IMPRoper CB CA N C
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END
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! ==ALA==
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remarks TORSIONS FOR AIB NOT AVAILABLE - AVOID USAGE
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! ==AIB==
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RESIdue AIB
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GROUp
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ATOM N TYPE= N CHARge= -0.570 END
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ATOM H TYPE= H CHARge= 0.370 END
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ATOM CA TYPE= C0 CHARge= 0.200 END
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ATOM C TYPE= C CHARge= 0.500 END
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ATOM O TYPE= O CHARge= -0.500 END
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ATOM CB1 TYPE= C3c CHARge= 0.000 END
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ATOM CB2 TYPE= C3c CHARge= 0.000 END
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BOND H N BOND CA N BOND C CA BOND O C
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BOND CB1 CA BOND CB2 CA
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DIHEdral C CA N H
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DIHEdral O C CA N
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DIHEdral CB1 CA N H
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DIHEdral CB1 CA C O
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DIHEdral CB2 CA N H
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END
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! ==AIB==
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! ==VAL==
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RESIdue VAL
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GROUp
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ATOM N TYPE= N CHARge= -0.570 END
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ATOM H TYPE= H CHARge= 0.370 END
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ATOM CA TYPE= CH CHARge= 0.200 END
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ATOM C TYPE= C CHARge= 0.500 END
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ATOM O TYPE= O CHARge= -0.500 END
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ATOM CB TYPE= CHa CHARge= 0.000 END
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ATOM CG1 TYPE= C3 CHARge= 0.000 END
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ATOM CG2 TYPE= C3 CHARge= 0.000 END
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BOND H N BOND CA N BOND C CA BOND O C
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BOND CB CA BOND CG1 CB BOND CG2 CB
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DIHEdral C CA N H
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DIHEdral O C CA N
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DIHEdral CB CA N H
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DIHEdral CB CA C O
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DIHEdral CG1 CB CA N MULT 3
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DIHEdral CG1 CB CA C MULT 3
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DIHEdral CG2 CB CA N MULT 3
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DIHEdral CG2 CB CA C MULT 3
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IMPRoper CB CA N C
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IMPRoper CG1 CB CA CG2
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END
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! ==VAL==
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! ==LEU==
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RESIdue LEU
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GROUp
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ATOM N TYPE= N CHARge= -0.570 END
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ATOM H TYPE= H CHARge= 0.370 END
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ATOM CA TYPE= CH CHARge= 0.200 END
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ATOM C TYPE= C CHARge= 0.500 END
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ATOM O TYPE= O CHARge= -0.500 END
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ATOM CB TYPE= C2a CHARge= 0.000 END
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ATOM CG TYPE= CHa CHARge= 0.000 END
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ATOM CD1 TYPE= C3 CHARge= 0.000 END
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ATOM CD2 TYPE= C3 CHARge= 0.000 END
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BOND H N BOND CA N BOND C CA BOND O C
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BOND CB CA BOND CG CB BOND CD1 CG BOND CD2 CG
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DIHEdral C CA N H
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DIHEdral O C CA N
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DIHEdral CB CA N H
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DIHEdral CB CA C O
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DIHEdral CG CB CA N MULT 3
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DIHEdral CG CB CA C MULT 3
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DIHEdral CD1 CG CB CA MULT 3
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DIHEdral CD2 CG CB CA MULT 3
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IMPRoper CB CA N C
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IMPRoper CD1 CG CB CD2
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END
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! ==LEU==
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! ==ILE==
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RESIdue ILE
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GROUp
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ATOM N TYPE= N CHARge= -0.570 END
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ATOM H TYPE= H CHARge= 0.370 END
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ATOM CA TYPE= CH CHARge= 0.200 END
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ATOM C TYPE= C CHARge= 0.500 END
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ATOM O TYPE= O CHARge= -0.500 END
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ATOM CB TYPE= CHa CHARge= 0.000 END
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ATOM CG1 TYPE= C2a CHARge= 0.000 END
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ATOM CG2 TYPE= C3 CHARge= 0.000 END
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|
+
ATOM CD1 TYPE= C3a CHARge= 0.000 END
|
|
236
|
+
|
|
237
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
238
|
+
BOND CB CA BOND CG1 CB BOND CG2 CB BOND CD1 CG1
|
|
239
|
+
|
|
240
|
+
DIHEdral C CA N H
|
|
241
|
+
DIHEdral O C CA N
|
|
242
|
+
DIHEdral CB CA N H
|
|
243
|
+
DIHEdral CB CA C O
|
|
244
|
+
DIHEdral CG1 CB CA N MULT 3
|
|
245
|
+
DIHEdral CG1 CB CA C MULT 3
|
|
246
|
+
DIHEdral CG2 CB CA N MULT 3
|
|
247
|
+
DIHEdral CG2 CB CA C MULT 3
|
|
248
|
+
DIHEdral CD1 CG1 CB CA MULT 3
|
|
249
|
+
DIHEdral CD1 CG1 CB CG2 MULT 3
|
|
250
|
+
|
|
251
|
+
IMPRoper CB CA N C
|
|
252
|
+
IMPRoper CG2 CB CA CG1
|
|
253
|
+
|
|
254
|
+
END
|
|
255
|
+
! ==ILE==
|
|
256
|
+
|
|
257
|
+
! ==PRO==
|
|
258
|
+
RESIdue PRO
|
|
259
|
+
GROUp
|
|
260
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
261
|
+
ATOM CA TYPE= CHp CHARge= 0.285 END
|
|
262
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
263
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
264
|
+
ATOM CB TYPE= C2a CHARge= 0.000 END
|
|
265
|
+
ATOM CG TYPE= C2a CHARge= 0.000 END
|
|
266
|
+
ATOM CD TYPE= C2p CHARge= 0.285 END
|
|
267
|
+
|
|
268
|
+
BOND CA N BOND C CA BOND O C
|
|
269
|
+
BOND CB CA BOND CG CB BOND CD CG BOND CD N
|
|
270
|
+
|
|
271
|
+
DIHEdral O C CA N
|
|
272
|
+
DIHEdral CB CA C O
|
|
273
|
+
DIHEdral CG CB CA N MULT 3
|
|
274
|
+
DIHEdral CG CB CA C MULT 3
|
|
275
|
+
DIHEdral CD CG CB CA MULT 3
|
|
276
|
+
DIHEdral CD N CA C MULT 3
|
|
277
|
+
DIHEdral CD N CA CB MULT 3
|
|
278
|
+
DIHEdral CG CD N CA MULT 3
|
|
279
|
+
DIHEdral CB CG CD N MULT 3
|
|
280
|
+
|
|
281
|
+
IMPRoper CB CA N C
|
|
282
|
+
|
|
283
|
+
END
|
|
284
|
+
! ==PRO==
|
|
285
|
+
|
|
286
|
+
! ==HYP==
|
|
287
|
+
RESIdue HYP
|
|
288
|
+
GROUp
|
|
289
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
290
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
291
|
+
ATOM CA TYPE= CHp CHARge= 0.285 END
|
|
292
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
293
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
294
|
+
ATOM CB TYPE= C2a CHARge= 0.000 END
|
|
295
|
+
ATOM CG TYPE= CHa CHARge= 0.265 END
|
|
296
|
+
ATOM CD1 TYPE= C2p CHARge= 0.285 END
|
|
297
|
+
ATOM OD2 TYPE= OH CHARge= -0.700 END
|
|
298
|
+
ATOM HD2 TYPE= HO CHARge= 0.435 END
|
|
299
|
+
|
|
300
|
+
BOND CA N BOND C CA BOND O C
|
|
301
|
+
BOND CB CA BOND CG CB BOND CD1 CG BOND CD1 N
|
|
302
|
+
BOND OD2 CG BOND HD2 OD2
|
|
303
|
+
|
|
304
|
+
DIHEdral O C CA N
|
|
305
|
+
DIHEdral CB CA C O
|
|
306
|
+
DIHEdral CG CB CA N MULT 3
|
|
307
|
+
DIHEdral CG CB CA C MULT 3
|
|
308
|
+
DIHEdral CD1 CG CB CA MULT 3
|
|
309
|
+
DIHEdral CD1 N CA C MULT 3
|
|
310
|
+
DIHEdral CD1 N CA CB MULT 3
|
|
311
|
+
DIHEdral CG CD1 N CA MULT 3
|
|
312
|
+
DIHEdral CB CG CD1 N MULT 3
|
|
313
|
+
DIHEdral OD2 CG CB CA MULT 3
|
|
314
|
+
DIHEdral OD2 CG CD1 N MULT 3
|
|
315
|
+
DIHEdral HD2 OD2 CG CB MULT 3
|
|
316
|
+
DIHEdral HD2 OD2 CG CD1 MULT 3
|
|
317
|
+
|
|
318
|
+
IMPRoper CB CA N C
|
|
319
|
+
IMPRoper OD2 CG CB CD1
|
|
320
|
+
|
|
321
|
+
END
|
|
322
|
+
! ==HYP==
|
|
323
|
+
|
|
324
|
+
! ==CYS==
|
|
325
|
+
RESIdue CYS
|
|
326
|
+
GROUp
|
|
327
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
328
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
329
|
+
ATOM CA TYPE= CH CHARge= 0.200 END
|
|
330
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
331
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
332
|
+
ATOM CB TYPE= C2a CHARge= 0.180 END
|
|
333
|
+
ATOM SG TYPE= SH CHARge= -0.450 END
|
|
334
|
+
ATOM HG TYPE= HS CHARge= 0.270 END
|
|
335
|
+
|
|
336
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
337
|
+
BOND CB CA BOND SG CB BOND HG SG
|
|
338
|
+
|
|
339
|
+
DIHEdral C CA N H
|
|
340
|
+
DIHEdral O C CA N
|
|
341
|
+
DIHEdral CB CA N H
|
|
342
|
+
DIHEdral CB CA C O
|
|
343
|
+
DIHEdral SG CB CA N MULT 3
|
|
344
|
+
DIHEdral SG CB CA C MULT 3
|
|
345
|
+
DIHEdral HG SG CB CA MULT 3
|
|
346
|
+
|
|
347
|
+
IMPRoper CB CA N C
|
|
348
|
+
|
|
349
|
+
END
|
|
350
|
+
! ==CYS==
|
|
351
|
+
|
|
352
|
+
! ==CYT==
|
|
353
|
+
RESIdue CYT
|
|
354
|
+
GROUp
|
|
355
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
356
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
357
|
+
ATOM CA TYPE= CH CHARge= 0.200 END
|
|
358
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
359
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
360
|
+
ATOM CB TYPE= C2 CHARge= 0.300 END
|
|
361
|
+
ATOM SG TYPE= S CHARge= -0.300 END
|
|
362
|
+
|
|
363
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
364
|
+
BOND CB CA BOND SG CB
|
|
365
|
+
|
|
366
|
+
DIHEdral C CA N H
|
|
367
|
+
DIHEdral O C CA N
|
|
368
|
+
DIHEdral CB CA N H
|
|
369
|
+
DIHEdral CB CA C O
|
|
370
|
+
DIHEdral SG CB CA N MULT 3
|
|
371
|
+
DIHEdral SG CB CA C MULT 3
|
|
372
|
+
|
|
373
|
+
IMPRoper CB CA N C
|
|
374
|
+
|
|
375
|
+
END
|
|
376
|
+
! ==CYT==
|
|
377
|
+
|
|
378
|
+
! ==MET==
|
|
379
|
+
RESIdue MET
|
|
380
|
+
GROUp
|
|
381
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
382
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
383
|
+
ATOM CA TYPE= CH CHARge= 0.200 END
|
|
384
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
385
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
386
|
+
ATOM CB TYPE= C2a CHARge= 0.000 END
|
|
387
|
+
ATOM CG TYPE= C2 CHARge= 0.235 END
|
|
388
|
+
ATOM SD TYPE= S CHARge= -0.470 END
|
|
389
|
+
ATOM CE TYPE= C3b CHARge= 0.235 END
|
|
390
|
+
|
|
391
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
392
|
+
BOND CB CA BOND CG CB BOND SD CG BOND CE SD
|
|
393
|
+
|
|
394
|
+
DIHEdral C CA N H
|
|
395
|
+
DIHEdral O C CA N
|
|
396
|
+
DIHEdral CB CA N H
|
|
397
|
+
DIHEdral CB CA C O
|
|
398
|
+
DIHEdral CG CB CA N MULT 3
|
|
399
|
+
DIHEdral CG CB CA C MULT 3
|
|
400
|
+
DIHEdral SD CG CB CA MULT 3
|
|
401
|
+
DIHEdral CE SD CG CB MULT 3
|
|
402
|
+
|
|
403
|
+
IMPRoper CB CA N C
|
|
404
|
+
|
|
405
|
+
END
|
|
406
|
+
! ==MET==
|
|
407
|
+
|
|
408
|
+
! ==SER==
|
|
409
|
+
RESIdue SER
|
|
410
|
+
GROUp
|
|
411
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
412
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
413
|
+
ATOM CA TYPE= CH CHARge= 0.200 END
|
|
414
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
415
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
416
|
+
ATOM CB TYPE= C2a CHARge= 0.265 END
|
|
417
|
+
ATOM OG TYPE= OH CHARge= -0.700 END
|
|
418
|
+
ATOM HG TYPE= HO CHARge= 0.435 END
|
|
419
|
+
|
|
420
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
421
|
+
BOND CB CA BOND OG CB BOND HG OG
|
|
422
|
+
|
|
423
|
+
DIHEdral C CA N H
|
|
424
|
+
DIHEdral O C CA N
|
|
425
|
+
DIHEdral CB CA N H
|
|
426
|
+
DIHEdral CB CA C O
|
|
427
|
+
DIHEdral OG CB CA N MULT 3
|
|
428
|
+
DIHEdral OG CB CA C MULT 3
|
|
429
|
+
DIHEdral HG OG CB CA MULT 3
|
|
430
|
+
|
|
431
|
+
IMPRoper CB CA N C
|
|
432
|
+
|
|
433
|
+
END
|
|
434
|
+
! ==SER==
|
|
435
|
+
|
|
436
|
+
! ==THR==
|
|
437
|
+
RESIdue THR
|
|
438
|
+
GROUp
|
|
439
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
440
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
441
|
+
ATOM CA TYPE= CH CHARge= 0.200 END
|
|
442
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
443
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
444
|
+
ATOM CB TYPE= CHa CHARge= 0.265 END
|
|
445
|
+
ATOM OG1 TYPE= OH CHARge= -0.700 END
|
|
446
|
+
ATOM HG1 TYPE= HO CHARge= 0.435 END
|
|
447
|
+
ATOM CG2 TYPE= C3 CHARge= 0.000 END
|
|
448
|
+
|
|
449
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
450
|
+
BOND CB CA BOND OG1 CB BOND CG2 CB BOND HG1 OG1
|
|
451
|
+
|
|
452
|
+
DIHEdral C CA N H
|
|
453
|
+
DIHEdral O C CA N
|
|
454
|
+
DIHEdral CB CA N H
|
|
455
|
+
DIHEdral CB CA C O
|
|
456
|
+
DIHEdral OG1 CB CA N MULT 3
|
|
457
|
+
DIHEdral OG1 CB CA C MULT 3
|
|
458
|
+
DIHEdral CG2 CB CA N MULT 3
|
|
459
|
+
DIHEdral CG2 CB CA C MULT 3
|
|
460
|
+
DIHEdral HG1 OG1 CB CA MULT 3
|
|
461
|
+
DIHEdral HG1 OG1 CB CG2 MULT 3
|
|
462
|
+
|
|
463
|
+
IMPRoper CB CA N C
|
|
464
|
+
IMPRoper CG2 CB CA OG1
|
|
465
|
+
|
|
466
|
+
END
|
|
467
|
+
! ==THR==
|
|
468
|
+
|
|
469
|
+
! ==ASP==
|
|
470
|
+
RESIdue ASP
|
|
471
|
+
GROUp
|
|
472
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
473
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
474
|
+
ATOM CA TYPE= CH CHARge= 0.200 END
|
|
475
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
476
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
477
|
+
ATOM CB TYPE= C2a CHARge= -0.100 END
|
|
478
|
+
ATOM CG TYPE= C CHARge= 0.700 END
|
|
479
|
+
ATOM OD1 TYPE= O2 CHARge= -0.800 END
|
|
480
|
+
ATOM OD2 TYPE= O2 CHARge= -0.800 END
|
|
481
|
+
|
|
482
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
483
|
+
BOND CB CA BOND CG CB BOND OD1 CG BOND OD2 CG
|
|
484
|
+
|
|
485
|
+
DIHEdral C CA N H
|
|
486
|
+
DIHEdral O C CA N
|
|
487
|
+
DIHEdral CB CA N H
|
|
488
|
+
DIHEdral CB CA C O
|
|
489
|
+
DIHEdral CG CB CA N MULT 3
|
|
490
|
+
DIHEdral CG CB CA C MULT 3
|
|
491
|
+
DIHEdral OD1 CG CB CA MULT 3
|
|
492
|
+
DIHEdral OD2 CG CB CA MULT 3
|
|
493
|
+
|
|
494
|
+
IMPRoper CB CA N C
|
|
495
|
+
IMPRoper CB OD1 CG OD2
|
|
496
|
+
|
|
497
|
+
END
|
|
498
|
+
! ==ASP==
|
|
499
|
+
|
|
500
|
+
! ==ASN==
|
|
501
|
+
RESIdue ASN
|
|
502
|
+
GROUp
|
|
503
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
504
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
505
|
+
ATOM CA TYPE= CH CHARge= 0.200 END
|
|
506
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
507
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
508
|
+
ATOM CB TYPE= C2a CHARge= 0.000 END
|
|
509
|
+
ATOM CG TYPE= C CHARge= 0.500 END
|
|
510
|
+
ATOM OD1 TYPE= O CHARge= -0.500 END
|
|
511
|
+
ATOM ND2 TYPE= N CHARge= -0.850 END
|
|
512
|
+
ATOM HD21 TYPE= Hb CHARge= 0.425 END
|
|
513
|
+
ATOM HD22 TYPE= Hb CHARge= 0.425 END
|
|
514
|
+
|
|
515
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
516
|
+
BOND CB CA BOND CG CB BOND OD1 CG BOND ND2 CG
|
|
517
|
+
BOND HD21 ND2 BOND HD22 ND2
|
|
518
|
+
|
|
519
|
+
DIHEdral C CA N H
|
|
520
|
+
DIHEdral O C CA N
|
|
521
|
+
DIHEdral CB CA N H
|
|
522
|
+
DIHEdral CB CA C O
|
|
523
|
+
DIHEdral CG CB CA N MULT 3
|
|
524
|
+
DIHEdral CG CB CA C MULT 3
|
|
525
|
+
DIHEdral OD1 CG CB CA
|
|
526
|
+
DIHEdral ND2 CG CB CA MULT 2
|
|
527
|
+
DIHEdral HD21 ND2 CG CB
|
|
528
|
+
DIHEdral HD21 ND2 CG OD1
|
|
529
|
+
DIHEdral HD22 ND2 CG CB
|
|
530
|
+
DIHEdral HD22 ND2 CG OD1
|
|
531
|
+
|
|
532
|
+
IMPRoper CB CA N C
|
|
533
|
+
IMPRoper CG ND2 CB OD1
|
|
534
|
+
IMPRoper CG HD21 ND2 HD22
|
|
535
|
+
|
|
536
|
+
END
|
|
537
|
+
! ==ASN==
|
|
538
|
+
|
|
539
|
+
! ==GLU==
|
|
540
|
+
RESIdue GLU
|
|
541
|
+
GROUp
|
|
542
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
543
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
544
|
+
ATOM CA TYPE= CH CHARge= 0.200 END
|
|
545
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
546
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
547
|
+
ATOM CB TYPE= C2a CHARge= 0.000 END
|
|
548
|
+
ATOM CG TYPE= C2a CHARge= -0.100 END
|
|
549
|
+
ATOM CD TYPE= C CHARge= 0.700 END
|
|
550
|
+
ATOM OE1 TYPE= O2 CHARge= -0.800 END
|
|
551
|
+
ATOM OE2 TYPE= O2 CHARge= -0.800 END
|
|
552
|
+
|
|
553
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
554
|
+
BOND CB CA BOND CG CB BOND CD CG BOND OE1 CD BOND OE2 CD
|
|
555
|
+
|
|
556
|
+
DIHEdral C CA N H
|
|
557
|
+
DIHEdral O C CA N
|
|
558
|
+
DIHEdral CB CA N H
|
|
559
|
+
DIHEdral CB CA C O
|
|
560
|
+
DIHEdral CG CB CA N MULT 3
|
|
561
|
+
DIHEdral CG CB CA C MULT 3
|
|
562
|
+
DIHEdral CD CG CB CA MULT 3
|
|
563
|
+
DIHEdral OE1 CD CG CB MULT 3
|
|
564
|
+
DIHEdral OE2 CD CG CB MULT 3
|
|
565
|
+
|
|
566
|
+
IMPRoper CB CA N C
|
|
567
|
+
IMPRoper CG OE1 CD OE2
|
|
568
|
+
|
|
569
|
+
END
|
|
570
|
+
! ==GLU==
|
|
571
|
+
|
|
572
|
+
! ==GLN==
|
|
573
|
+
RESIdue GLN
|
|
574
|
+
GROUp
|
|
575
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
576
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
577
|
+
ATOM CA TYPE= CH CHARge= 0.200 END
|
|
578
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
579
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
580
|
+
ATOM CB TYPE= C2a CHARge= 0.000 END
|
|
581
|
+
ATOM CG TYPE= C2a CHARge= 0.000 END
|
|
582
|
+
ATOM CD TYPE= C CHARge= 0.500 END
|
|
583
|
+
ATOM OE1 TYPE= O CHARge= -0.500 END
|
|
584
|
+
ATOM NE2 TYPE= N CHARge= -0.850 END
|
|
585
|
+
ATOM HE21 TYPE= Hb CHARge= 0.425 END
|
|
586
|
+
ATOM HE22 TYPE= Hb CHARge= 0.425 END
|
|
587
|
+
|
|
588
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
589
|
+
BOND CB CA BOND CG CB BOND CD CG BOND OE1 CD
|
|
590
|
+
BOND NE2 CD BOND HE21 NE2 BOND HE22 NE2
|
|
591
|
+
|
|
592
|
+
DIHEdral C CA N H
|
|
593
|
+
DIHEdral O C CA N
|
|
594
|
+
DIHEdral CB CA N H
|
|
595
|
+
DIHEdral CB CA C O
|
|
596
|
+
DIHEdral CG CB CA N MULT 3
|
|
597
|
+
DIHEdral CG CB CA C MULT 3
|
|
598
|
+
DIHEdral CD CG CB CA MULT 3
|
|
599
|
+
DIHEdral OE1 CD CG CB
|
|
600
|
+
DIHEdral NE2 CD CG CB MULT 2
|
|
601
|
+
DIHEdral HE21 NE2 CD CG
|
|
602
|
+
DIHEdral HE21 NE2 CD OE1
|
|
603
|
+
DIHEdral HE22 NE2 CD CG
|
|
604
|
+
DIHEdral HE22 NE2 CD OE1
|
|
605
|
+
|
|
606
|
+
IMPRoper CB CA N C
|
|
607
|
+
IMPRoper CD NE2 CG OE1
|
|
608
|
+
IMPRoper CD HE21 NE2 HE22
|
|
609
|
+
|
|
610
|
+
END
|
|
611
|
+
! ==GLN==
|
|
612
|
+
|
|
613
|
+
! ==LYS==
|
|
614
|
+
RESIdue LYS
|
|
615
|
+
GROUp
|
|
616
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
617
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
618
|
+
ATOM CA TYPE= CH CHARge= 0.200 END
|
|
619
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
620
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
621
|
+
ATOM CB TYPE= C2a CHARge= 0.000 END
|
|
622
|
+
ATOM CG TYPE= C2a CHARge= 0.000 END
|
|
623
|
+
ATOM CD TYPE= C2a CHARge= 0.000 END
|
|
624
|
+
ATOM CE TYPE= C2a CHARge= 0.310 END
|
|
625
|
+
ATOM NZ TYPE= N3 CHARge= -0.300 END
|
|
626
|
+
ATOM HZ1 TYPE= H3 CHARge= 0.330 END
|
|
627
|
+
ATOM HZ2 TYPE= H3 CHARge= 0.330 END
|
|
628
|
+
ATOM HZ3 TYPE= H3 CHARge= 0.330 END
|
|
629
|
+
|
|
630
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
631
|
+
BOND CB CA BOND CG CB BOND CD CG BOND CE CD
|
|
632
|
+
BOND NZ CE BOND HZ1 NZ BOND HZ2 NZ BOND HZ3 NZ
|
|
633
|
+
|
|
634
|
+
DIHEdral C CA N H
|
|
635
|
+
DIHEdral O C CA N
|
|
636
|
+
DIHEdral CB CA N H
|
|
637
|
+
DIHEdral CB CA C O
|
|
638
|
+
DIHEdral CG CB CA N MULT 3
|
|
639
|
+
DIHEdral CG CB CA C MULT 3
|
|
640
|
+
DIHEdral CD CG CB CA MULT 3
|
|
641
|
+
DIHEdral CE CD CG CB MULT 3
|
|
642
|
+
DIHEdral NZ CE CD CG MULT 3
|
|
643
|
+
DIHEdral HZ1 NZ CE CD
|
|
644
|
+
DIHEdral HZ2 NZ CE CD
|
|
645
|
+
DIHEdral HZ3 NZ CE CD
|
|
646
|
+
|
|
647
|
+
IMPRoper CB CA N C
|
|
648
|
+
|
|
649
|
+
END
|
|
650
|
+
! ==LYS==
|
|
651
|
+
|
|
652
|
+
! ==HYL==
|
|
653
|
+
RESIdue HYL
|
|
654
|
+
GROUp
|
|
655
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
656
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
657
|
+
ATOM CA TYPE= CH CHARge= 0.200 END
|
|
658
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
659
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
660
|
+
ATOM CB TYPE= C2a CHARge= 0.000 END
|
|
661
|
+
ATOM CG TYPE= C2a CHARge= 0.000 END
|
|
662
|
+
ATOM CD TYPE= CHa CHARge= 0.265 END
|
|
663
|
+
ATOM CE1 TYPE= C2a CHARge= 0.310 END
|
|
664
|
+
ATOM OE2 TYPE= OH CHARge= -0.700 END
|
|
665
|
+
ATOM HE2 TYPE= HO CHARge= 0.435 END
|
|
666
|
+
ATOM NZ1 TYPE= N3 CHARge= -0.300 END
|
|
667
|
+
ATOM HZ11 TYPE= H3 CHARge= 0.330 END
|
|
668
|
+
ATOM HZ12 TYPE= H3 CHARge= 0.330 END
|
|
669
|
+
ATOM HZ13 TYPE= H3 CHARge= 0.330 END
|
|
670
|
+
|
|
671
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
672
|
+
BOND CB CA BOND CG CB BOND CD CG BOND CE1 CD
|
|
673
|
+
BOND OE2 CD BOND HE2 OE2 BOND NZ1 CE1 BOND HZ11 NZ1
|
|
674
|
+
BOND HZ12 NZ1 BOND HZ13 NZ1
|
|
675
|
+
|
|
676
|
+
DIHEdral C CA N H
|
|
677
|
+
DIHEdral O C CA N
|
|
678
|
+
DIHEdral CB CA N H
|
|
679
|
+
DIHEdral CB CA C O
|
|
680
|
+
DIHEdral CG CB CA N MULT 3
|
|
681
|
+
DIHEdral CG CB CA C MULT 3
|
|
682
|
+
DIHEdral CD CG CB CA MULT 3
|
|
683
|
+
DIHEdral CE1 CD CG CB MULT 3
|
|
684
|
+
DIHEdral OE2 CD CG CB MULT 3
|
|
685
|
+
DIHEdral HE2 OE2 CD CG MULT 3
|
|
686
|
+
DIHEdral HE2 OE2 CD CE1 MULT 3
|
|
687
|
+
DIHEdral NZ1 CE1 CD CG MULT 3
|
|
688
|
+
DIHEdral NZ1 CE1 CD OE2 MULT 3
|
|
689
|
+
DIHEdral HZ11 NZ1 CE1 CD
|
|
690
|
+
DIHEdral HZ12 NZ1 CE1 CD
|
|
691
|
+
DIHEdral HZ13 NZ1 CE1 CD
|
|
692
|
+
|
|
693
|
+
IMPRoper CB CA N C
|
|
694
|
+
IMPRoper CG CE1 CD OE2
|
|
695
|
+
|
|
696
|
+
END
|
|
697
|
+
! ==HYL==
|
|
698
|
+
|
|
699
|
+
! ==ARG==
|
|
700
|
+
RESIdue ARG
|
|
701
|
+
GROUp
|
|
702
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
703
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
704
|
+
ATOM CA TYPE= CH CHARge= 0.200 END
|
|
705
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
706
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
707
|
+
ATOM CB TYPE= C2a CHARge= 0.000 END
|
|
708
|
+
ATOM CG TYPE= C2a CHARge= 0.070 END
|
|
709
|
+
ATOM CD TYPE= C2a CHARge= 0.310 END
|
|
710
|
+
ATOM NE TYPE= N2 CHARge= -0.700 END
|
|
711
|
+
ATOM HE TYPE= H3 CHARge= 0.440 END
|
|
712
|
+
ATOM CZ TYPE= CAa CHARge= 0.640 END
|
|
713
|
+
ATOM NH1 TYPE= N2 CHARge= -0.800 END
|
|
714
|
+
ATOM NH2 TYPE= N2 CHARge= -0.800 END
|
|
715
|
+
ATOM HH11 TYPE= H3 CHARge= 0.460 END
|
|
716
|
+
ATOM HH12 TYPE= H3 CHARge= 0.460 END
|
|
717
|
+
ATOM HH21 TYPE= H3 CHARge= 0.460 END
|
|
718
|
+
ATOM HH22 TYPE= H3 CHARge= 0.460 END
|
|
719
|
+
|
|
720
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
721
|
+
BOND CB CA BOND CG CB BOND CD CG BOND NE CD
|
|
722
|
+
BOND HE NE BOND CZ NE BOND NH1 CZ BOND NH2 CZ
|
|
723
|
+
BOND HH11 NH1 BOND HH12 NH1 BOND HH21 NH2 BOND HH22 NH2
|
|
724
|
+
|
|
725
|
+
DIHEdral C CA N H
|
|
726
|
+
DIHEdral O C CA N
|
|
727
|
+
DIHEdral CB CA N H
|
|
728
|
+
DIHEdral CB CA C O
|
|
729
|
+
DIHEdral CG CB CA N MULT 3
|
|
730
|
+
DIHEdral CG CB CA C MULT 3
|
|
731
|
+
DIHEdral CD CG CB CA MULT 3
|
|
732
|
+
DIHEdral NE CD CG CB MULT 3
|
|
733
|
+
DIHEdral HE NE CD CG
|
|
734
|
+
DIHEdral CZ NE CD CG MULT 3
|
|
735
|
+
DIHEdral NH1 CZ NE CD
|
|
736
|
+
DIHEdral NH1 CZ NE HE
|
|
737
|
+
DIHEdral NH2 CZ NE CD
|
|
738
|
+
DIHEdral NH2 CZ NE HE
|
|
739
|
+
DIHEdral HH11 NH1 CZ NE
|
|
740
|
+
DIHEdral HH11 NH1 CZ NH2
|
|
741
|
+
DIHEdral HH12 NH1 CZ NE
|
|
742
|
+
DIHEdral HH12 NH1 CZ NH2
|
|
743
|
+
DIHEdral HH21 NH2 CZ NE
|
|
744
|
+
DIHEdral HH21 NH2 CZ NH1
|
|
745
|
+
DIHEdral HH22 NH2 CZ NE
|
|
746
|
+
DIHEdral HH22 NH2 CZ NH1
|
|
747
|
+
|
|
748
|
+
IMPRoper CB CA N C
|
|
749
|
+
IMPRoper NE NH1 CZ NH2
|
|
750
|
+
IMPRoper NE CZ CD HE
|
|
751
|
+
IMPRoper HH12 NH1 CZ HH11
|
|
752
|
+
IMPRoper HH22 NH2 CZ HH21
|
|
753
|
+
|
|
754
|
+
END
|
|
755
|
+
! ==ARG==
|
|
756
|
+
|
|
757
|
+
! ==HID==
|
|
758
|
+
RESIdue HID
|
|
759
|
+
GROUp
|
|
760
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
761
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
762
|
+
ATOM CA TYPE= CH CHARge= 0.200 END
|
|
763
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
764
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
765
|
+
ATOM CB TYPE= C2 CHARge= 0.115 END
|
|
766
|
+
ATOM CG TYPE= CA CHARge= 0.015 END
|
|
767
|
+
ATOM ND1 TYPE= NA CHARge= -0.570 END
|
|
768
|
+
ATOM CD2 TYPE= CA CHARge= -0.015 END
|
|
769
|
+
ATOM CE1 TYPE= CA CHARge= 0.295 END
|
|
770
|
+
ATOM NE2 TYPE= NB CHARge= -0.490 END
|
|
771
|
+
ATOM HD1 TYPE= H CHARge= 0.420 END
|
|
772
|
+
ATOM HD2 TYPE= HC CHARge= 0.115 END
|
|
773
|
+
ATOM HE1 TYPE= HC CHARge= 0.115 END
|
|
774
|
+
|
|
775
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
776
|
+
BOND CB CA BOND CG CB BOND ND1 CG BOND CD2 CG
|
|
777
|
+
BOND CE1 ND1 BOND NE2 CD2 BOND NE2 CE1 BOND HD1 ND1
|
|
778
|
+
BOND HD2 CD2 BOND HE1 CE1
|
|
779
|
+
|
|
780
|
+
DIHEdral C CA N H
|
|
781
|
+
DIHEdral O C CA N
|
|
782
|
+
DIHEdral CB CA N H
|
|
783
|
+
DIHEdral CB CA C O
|
|
784
|
+
DIHEdral CG CB CA N MULT 3
|
|
785
|
+
DIHEdral CG CB CA C MULT 3
|
|
786
|
+
DIHEdral ND1 CG CB CA MULT 3
|
|
787
|
+
DIHEdral CD2 CG CB CA MULT 3
|
|
788
|
+
DIHEdral CE1 ND1 CG CB
|
|
789
|
+
DIHEdral CE1 ND1 CG CD2
|
|
790
|
+
DIHEdral NE2 CD2 CG CB
|
|
791
|
+
DIHEdral NE2 CD2 CG ND1
|
|
792
|
+
DIHEdral NE2 CE1 ND1 CG
|
|
793
|
+
DIHEdral ND1 CE1 NE2 CD2
|
|
794
|
+
DIHEdral CE1 NE2 CD2 CG
|
|
795
|
+
DIHEdral HD1 ND1 CG CB
|
|
796
|
+
DIHEdral HD1 ND1 CG CD2
|
|
797
|
+
DIHEdral HD1 ND1 CE1 NE2
|
|
798
|
+
DIHEdral HD2 CD2 CG CB
|
|
799
|
+
DIHEdral HD2 CD2 CG ND1
|
|
800
|
+
DIHEdral HD2 CD2 NE2 CE1
|
|
801
|
+
DIHEdral HE1 CE1 ND1 CG
|
|
802
|
+
DIHEdral HE1 CE1 ND1 HD1
|
|
803
|
+
DIHEdral HE1 CE1 NE2 CD2
|
|
804
|
+
|
|
805
|
+
IMPRoper CB CA N C
|
|
806
|
+
IMPRoper CG CE1 ND1 HD1
|
|
807
|
+
IMPRoper CB ND1 CG CD2
|
|
808
|
+
IMPRoper CG NE2 CD2 HD2
|
|
809
|
+
IMPRoper NE2 ND1 CE1 HE1
|
|
810
|
+
|
|
811
|
+
END
|
|
812
|
+
! ==HID==
|
|
813
|
+
|
|
814
|
+
! ==HIS==
|
|
815
|
+
RESIdue HIS
|
|
816
|
+
GROUp
|
|
817
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
818
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
819
|
+
ATOM CA TYPE= CH CHARge= 0.200 END
|
|
820
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
821
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
822
|
+
ATOM CB TYPE= C2 CHARge= 0.115 END
|
|
823
|
+
ATOM CG TYPE= CA CHARge= -0.015 END
|
|
824
|
+
ATOM ND1 TYPE= NB CHARge= -0.490 END
|
|
825
|
+
ATOM CD2 TYPE= CA CHARge= 0.015 END
|
|
826
|
+
ATOM CE1 TYPE= CA CHARge= 0.295 END
|
|
827
|
+
ATOM NE2 TYPE= NA CHARge= -0.570 END
|
|
828
|
+
ATOM HD2 TYPE= HC CHARge= 0.115 END
|
|
829
|
+
ATOM HE1 TYPE= HC CHARge= 0.115 END
|
|
830
|
+
ATOM HE2 TYPE= H CHARge= 0.420 END
|
|
831
|
+
|
|
832
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
833
|
+
BOND CB CA BOND CG CB BOND ND1 CG BOND CD2 CG
|
|
834
|
+
BOND CE1 ND1 BOND NE2 CD2 BOND NE2 CE1 BOND HD2 CD2
|
|
835
|
+
BOND HE1 CE1 BOND HE2 NE2
|
|
836
|
+
|
|
837
|
+
DIHEdral C CA N H
|
|
838
|
+
DIHEdral O C CA N
|
|
839
|
+
DIHEdral CB CA N H
|
|
840
|
+
DIHEdral CB CA C O
|
|
841
|
+
DIHEdral CG CB CA N MULT 3
|
|
842
|
+
DIHEdral CG CB CA C MULT 3
|
|
843
|
+
DIHEdral ND1 CG CB CA MULT 3
|
|
844
|
+
DIHEdral CD2 CG CB CA MULT 3
|
|
845
|
+
DIHEdral CE1 ND1 CG CB
|
|
846
|
+
DIHEdral CE1 ND1 CG CD2
|
|
847
|
+
DIHEdral NE2 CD2 CG CB
|
|
848
|
+
DIHEdral NE2 CD2 CG ND1
|
|
849
|
+
DIHEdral NE2 CE1 ND1 CG
|
|
850
|
+
DIHEdral ND1 CE1 NE2 CD2
|
|
851
|
+
DIHEdral CE1 NE2 CD2 CG
|
|
852
|
+
DIHEdral HD2 CD2 CG CB
|
|
853
|
+
DIHEdral HD2 CD2 CG ND1
|
|
854
|
+
DIHEdral HD2 CD2 NE2 CE1
|
|
855
|
+
DIHEdral HE1 CE1 ND1 CG
|
|
856
|
+
DIHEdral HE1 CE1 NE2 CD2
|
|
857
|
+
DIHEdral HE2 NE2 CD2 CG
|
|
858
|
+
DIHEdral HE2 NE2 CD2 HD2
|
|
859
|
+
DIHEdral HE2 NE2 CE1 ND1
|
|
860
|
+
DIHEdral HE2 NE2 CE1 HE1
|
|
861
|
+
|
|
862
|
+
IMPRoper CB CA N C
|
|
863
|
+
IMPRoper CE1 CD2 NE2 HE2
|
|
864
|
+
IMPRoper CB ND1 CG CD2
|
|
865
|
+
IMPRoper CG NE2 CD2 HD2
|
|
866
|
+
IMPRoper NE2 ND1 CE1 HE1
|
|
867
|
+
|
|
868
|
+
END
|
|
869
|
+
! ==HIS==
|
|
870
|
+
|
|
871
|
+
! ==HIP==
|
|
872
|
+
RESIdue HIP
|
|
873
|
+
GROUp
|
|
874
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
875
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
876
|
+
ATOM CA TYPE= CH CHARge= 0.200 END
|
|
877
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
878
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
879
|
+
ATOM CB TYPE= C2 CHARge= 0.115 END
|
|
880
|
+
ATOM CG TYPE= CA CHARge= 0.215 END
|
|
881
|
+
ATOM ND1 TYPE= NA CHARge= -0.540 END
|
|
882
|
+
ATOM CD2 TYPE= CA CHARge= 0.215 END
|
|
883
|
+
ATOM CE1 TYPE= CA CHARge= 0.385 END
|
|
884
|
+
ATOM NE2 TYPE= NA CHARge= -0.540 END
|
|
885
|
+
ATOM HD1 TYPE= H CHARge= 0.460 END
|
|
886
|
+
ATOM HD2 TYPE= HC CHARge= 0.115 END
|
|
887
|
+
ATOM HE1 TYPE= HC CHARge= 0.115 END
|
|
888
|
+
ATOM HE2 TYPE= H CHARge= 0.460 END
|
|
889
|
+
|
|
890
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
891
|
+
BOND CB CA BOND CG CB BOND ND1 CG BOND CD2 CG
|
|
892
|
+
BOND CE1 ND1 BOND NE2 CD2 BOND NE2 CE1 BOND HD1 ND1
|
|
893
|
+
BOND HD2 CD2 BOND HE1 CE1 BOND HE2 NE2
|
|
894
|
+
|
|
895
|
+
DIHEdral C CA N H
|
|
896
|
+
DIHEdral O C CA N
|
|
897
|
+
DIHEdral CB CA N H
|
|
898
|
+
DIHEdral CB CA C O
|
|
899
|
+
DIHEdral CG CB CA N MULT 3
|
|
900
|
+
DIHEdral CG CB CA C MULT 3
|
|
901
|
+
DIHEdral ND1 CG CB CA MULT 3
|
|
902
|
+
DIHEdral CD2 CG CB CA MULT 3
|
|
903
|
+
DIHEdral CE1 ND1 CG CB
|
|
904
|
+
DIHEdral CE1 ND1 CG CD2
|
|
905
|
+
DIHEdral NE2 CD2 CG CB
|
|
906
|
+
DIHEdral NE2 CD2 CG ND1
|
|
907
|
+
DIHEdral NE2 CE1 ND1 CG
|
|
908
|
+
DIHEdral ND1 CE1 NE2 CD2
|
|
909
|
+
DIHEdral CE1 NE2 CD2 CG
|
|
910
|
+
DIHEdral HD1 ND1 CG CB
|
|
911
|
+
DIHEdral HD1 ND1 CG CD2
|
|
912
|
+
DIHEdral HD1 ND1 CE1 NE2
|
|
913
|
+
DIHEdral HD2 CD2 CG CB
|
|
914
|
+
DIHEdral HD2 CD2 CG ND1
|
|
915
|
+
DIHEdral HD2 CD2 NE2 CE1
|
|
916
|
+
DIHEdral HE1 CE1 ND1 CG
|
|
917
|
+
DIHEdral HE1 CE1 ND1 HD1
|
|
918
|
+
DIHEdral HE1 CE1 NE2 CD2
|
|
919
|
+
DIHEdral HE2 NE2 CD2 CG
|
|
920
|
+
DIHEdral HE2 NE2 CD2 HD2
|
|
921
|
+
DIHEdral HE2 NE2 CE1 ND1
|
|
922
|
+
DIHEdral HE2 NE2 CE1 HE1
|
|
923
|
+
|
|
924
|
+
IMPRoper CB CA N C
|
|
925
|
+
IMPRoper CB ND1 CG CD2
|
|
926
|
+
IMPRoper HD1 ND1 CE1 CG
|
|
927
|
+
IMPRoper HE2 NE2 CD2 CE1
|
|
928
|
+
IMPRoper CG NE2 CD2 HD2
|
|
929
|
+
IMPRoper NE2 ND1 CE1 HE1
|
|
930
|
+
|
|
931
|
+
END
|
|
932
|
+
! ==HIP==
|
|
933
|
+
|
|
934
|
+
! ==PHE==
|
|
935
|
+
RESIdue PHE
|
|
936
|
+
GROUp
|
|
937
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
938
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
939
|
+
ATOM CA TYPE= CH CHARge= 0.200 END
|
|
940
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
941
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
942
|
+
ATOM CB TYPE= C2 CHARge= 0.115 END
|
|
943
|
+
ATOM CG TYPE= CA CHARge= -0.115 END
|
|
944
|
+
ATOM CD1 TYPE= CA CHARge= -0.115 END
|
|
945
|
+
ATOM CD2 TYPE= CA CHARge= -0.115 END
|
|
946
|
+
ATOM CE1 TYPE= CA CHARge= -0.115 END
|
|
947
|
+
ATOM CE2 TYPE= CA CHARge= -0.115 END
|
|
948
|
+
ATOM CZ TYPE= CA CHARge= -0.115 END
|
|
949
|
+
ATOM HD1 TYPE= HC CHARge= 0.115 END
|
|
950
|
+
ATOM HD2 TYPE= HC CHARge= 0.115 END
|
|
951
|
+
ATOM HE1 TYPE= HC CHARge= 0.115 END
|
|
952
|
+
ATOM HE2 TYPE= HC CHARge= 0.115 END
|
|
953
|
+
ATOM HZ TYPE= HC CHARge= 0.115 END
|
|
954
|
+
|
|
955
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
956
|
+
BOND CB CA BOND CG CB BOND CD1 CG BOND CD2 CG
|
|
957
|
+
BOND CE1 CD1 BOND CE2 CD2 BOND CZ CE1 BOND CZ CE2
|
|
958
|
+
BOND HD1 CD1 BOND HD2 CD2 BOND HE1 CE1 BOND HE2 CE2
|
|
959
|
+
BOND HZ CZ
|
|
960
|
+
|
|
961
|
+
DIHEdral C CA N H
|
|
962
|
+
DIHEdral O C CA N
|
|
963
|
+
DIHEdral CB CA N H
|
|
964
|
+
DIHEdral CB CA C O
|
|
965
|
+
DIHEdral CG CB CA N MULT 3
|
|
966
|
+
DIHEdral CG CB CA C MULT 3
|
|
967
|
+
DIHEdral CD1 CG CB CA MULT 3
|
|
968
|
+
DIHEdral CD2 CG CB CA MULT 3
|
|
969
|
+
DIHEdral CE1 CD1 CG CB
|
|
970
|
+
DIHEdral CE1 CD1 CG CD2
|
|
971
|
+
DIHEdral CE2 CD2 CG CB
|
|
972
|
+
DIHEdral CE2 CD2 CG CD1
|
|
973
|
+
DIHEdral CZ CE1 CD1 CG
|
|
974
|
+
DIHEdral CZ CE2 CD2 CG
|
|
975
|
+
DIHEdral CE1 CZ CE2 CD2
|
|
976
|
+
DIHEdral CE2 CZ CE1 CD1
|
|
977
|
+
DIHEdral HD1 CD1 CG CB
|
|
978
|
+
DIHEdral HD1 CD1 CG CD2
|
|
979
|
+
DIHEdral HD1 CD1 CE1 CZ
|
|
980
|
+
DIHEdral HD2 CD2 CG CB
|
|
981
|
+
DIHEdral HD2 CD2 CG CD1
|
|
982
|
+
DIHEdral HD2 CD2 CE2 CZ
|
|
983
|
+
DIHEdral HE1 CE1 CD1 CG
|
|
984
|
+
DIHEdral HE1 CE1 CD1 HD1
|
|
985
|
+
DIHEdral HE1 CE1 CZ CE2
|
|
986
|
+
DIHEdral HE2 CE2 CD2 CG
|
|
987
|
+
DIHEdral HE2 CE2 CD2 HD2
|
|
988
|
+
DIHEdral HE2 CE2 CZ CE1
|
|
989
|
+
DIHEdral HZ CZ CE1 CD1
|
|
990
|
+
DIHEdral HZ CZ CE1 HE1
|
|
991
|
+
DIHEdral HZ CZ CE2 CD2
|
|
992
|
+
DIHEdral HZ CZ CE2 HE2
|
|
993
|
+
|
|
994
|
+
IMPRoper CB CA N C
|
|
995
|
+
IMPRoper CD1 CG CD2 CB
|
|
996
|
+
IMPRoper CG CE1 CD1 HD1
|
|
997
|
+
IMPRoper CE2 CG CD2 HD2
|
|
998
|
+
IMPRoper CD1 CZ CE1 HE1
|
|
999
|
+
IMPRoper CZ CD2 CE2 HE2
|
|
1000
|
+
IMPRoper CE1 CE2 CZ HZ
|
|
1001
|
+
|
|
1002
|
+
END
|
|
1003
|
+
! ==PHE==
|
|
1004
|
+
|
|
1005
|
+
! ==TYR==
|
|
1006
|
+
RESIdue TYR
|
|
1007
|
+
GROUp
|
|
1008
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
1009
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
1010
|
+
ATOM CA TYPE= CH CHARge= 0.200 END
|
|
1011
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
1012
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
1013
|
+
ATOM CB TYPE= C2 CHARge= 0.115 END
|
|
1014
|
+
ATOM CG TYPE= CA CHARge= -0.115 END
|
|
1015
|
+
ATOM CD1 TYPE= CA CHARge= -0.115 END
|
|
1016
|
+
ATOM CD2 TYPE= CA CHARge= -0.115 END
|
|
1017
|
+
ATOM CE1 TYPE= CA CHARge= -0.115 END
|
|
1018
|
+
ATOM CE2 TYPE= CA CHARge= -0.115 END
|
|
1019
|
+
ATOM CZ TYPE= CAb CHARge= 0.150 END
|
|
1020
|
+
ATOM HD1 TYPE= HC CHARge= 0.115 END
|
|
1021
|
+
ATOM HD2 TYPE= HC CHARge= 0.115 END
|
|
1022
|
+
ATOM HE1 TYPE= HC CHARge= 0.115 END
|
|
1023
|
+
ATOM HE2 TYPE= HC CHARge= 0.115 END
|
|
1024
|
+
ATOM OH TYPE= OH CHARge= -0.585 END
|
|
1025
|
+
ATOM HH TYPE= HO CHARge= 0.435 END
|
|
1026
|
+
|
|
1027
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
1028
|
+
BOND CB CA BOND CG CB BOND CD1 CG BOND CD2 CG
|
|
1029
|
+
BOND CE1 CD1 BOND CE2 CD2 BOND CZ CE1 BOND CZ CE2
|
|
1030
|
+
BOND HD1 CD1 BOND HD2 CD2 BOND HE1 CE1 BOND HE2 CE2
|
|
1031
|
+
BOND OH CZ BOND HH OH
|
|
1032
|
+
|
|
1033
|
+
DIHEdral C CA N H
|
|
1034
|
+
DIHEdral O C CA N
|
|
1035
|
+
DIHEdral CB CA N H
|
|
1036
|
+
DIHEdral CB CA C O
|
|
1037
|
+
DIHEdral CG CB CA N MULT 3
|
|
1038
|
+
DIHEdral CG CB CA C MULT 3
|
|
1039
|
+
DIHEdral CD1 CG CB CA MULT 3
|
|
1040
|
+
DIHEdral CD2 CG CB CA MULT 3
|
|
1041
|
+
DIHEdral CE1 CD1 CG CB
|
|
1042
|
+
DIHEdral CE1 CD1 CG CD2
|
|
1043
|
+
DIHEdral CE2 CD2 CG CB
|
|
1044
|
+
DIHEdral CE2 CD2 CG CD1
|
|
1045
|
+
DIHEdral CZ CE1 CD1 CG
|
|
1046
|
+
DIHEdral CZ CE2 CD2 CG
|
|
1047
|
+
DIHEdral CE1 CZ CE2 CD2
|
|
1048
|
+
DIHEdral CE2 CZ CE1 CD1
|
|
1049
|
+
DIHEdral HD1 CD1 CG CB
|
|
1050
|
+
DIHEdral HD1 CD1 CG CD2
|
|
1051
|
+
DIHEdral HD1 CD1 CE1 CZ
|
|
1052
|
+
DIHEdral HD2 CD2 CG CB
|
|
1053
|
+
DIHEdral HD2 CD2 CG CD1
|
|
1054
|
+
DIHEdral HD2 CD2 CE2 CZ
|
|
1055
|
+
DIHEdral HE1 CE1 CD1 CG
|
|
1056
|
+
DIHEdral HE1 CE1 CD1 HD1
|
|
1057
|
+
DIHEdral HE1 CE1 CZ CE2
|
|
1058
|
+
DIHEdral HE2 CE2 CD2 CG
|
|
1059
|
+
DIHEdral HE2 CE2 CD2 HD2
|
|
1060
|
+
DIHEdral HE2 CE2 CZ CE1
|
|
1061
|
+
DIHEdral OH CZ CE1 CD1
|
|
1062
|
+
DIHEdral OH CZ CE1 HE1
|
|
1063
|
+
DIHEdral OH CZ CE2 CD2
|
|
1064
|
+
DIHEdral OH CZ CE2 HE2
|
|
1065
|
+
DIHEdral HH OH CZ CE1 MULT 3
|
|
1066
|
+
DIHEdral HH OH CZ CE2 MULT 3
|
|
1067
|
+
|
|
1068
|
+
IMPRoper CB CA N C
|
|
1069
|
+
IMPRoper CD1 CG CB CD2
|
|
1070
|
+
IMPRoper CG CE1 CD1 HD1
|
|
1071
|
+
IMPRoper CE2 CG CD2 HD2
|
|
1072
|
+
IMPRoper CD1 CZ CE1 HE1
|
|
1073
|
+
IMPRoper CZ CD2 CE2 HE2
|
|
1074
|
+
IMPRoper CE1 CE2 CZ OH
|
|
1075
|
+
|
|
1076
|
+
END
|
|
1077
|
+
! ==TYR==
|
|
1078
|
+
|
|
1079
|
+
! ==TRP==
|
|
1080
|
+
RESIdue TRP
|
|
1081
|
+
GROUp
|
|
1082
|
+
ATOM N TYPE= N CHARge= -0.570 END
|
|
1083
|
+
ATOM H TYPE= H CHARge= 0.370 END
|
|
1084
|
+
ATOM CA TYPE= CH CHARge= 0.200 END
|
|
1085
|
+
ATOM C TYPE= C CHARge= 0.500 END
|
|
1086
|
+
ATOM O TYPE= O CHARge= -0.500 END
|
|
1087
|
+
ATOM CB TYPE= C2 CHARge= 0.115 END
|
|
1088
|
+
ATOM CG TYPE= CA CHARge= -0.170 END
|
|
1089
|
+
ATOM CD1 TYPE= CA CHARge= 0.015 END
|
|
1090
|
+
ATOM CD2 TYPE= CB CHARge= -0.055 END
|
|
1091
|
+
ATOM NE1 TYPE= NA CHARge= -0.570 END
|
|
1092
|
+
ATOM CE2 TYPE= CC CHARge= 0.130 END
|
|
1093
|
+
ATOM CE3 TYPE= CA CHARge= -0.115 END
|
|
1094
|
+
ATOM CZ2 TYPE= CA CHARge= -0.115 END
|
|
1095
|
+
ATOM CZ3 TYPE= CA CHARge= -0.115 END
|
|
1096
|
+
ATOM CH2 TYPE= CA CHARge= -0.115 END
|
|
1097
|
+
ATOM HD1 TYPE= HC CHARge= 0.115 END
|
|
1098
|
+
ATOM HE1 TYPE= H CHARge= 0.420 END
|
|
1099
|
+
ATOM HE3 TYPE= HC CHARge= 0.115 END
|
|
1100
|
+
ATOM HZ2 TYPE= HC CHARge= 0.115 END
|
|
1101
|
+
ATOM HZ3 TYPE= HC CHARge= 0.115 END
|
|
1102
|
+
ATOM HH2 TYPE= HC CHARge= 0.115 END
|
|
1103
|
+
|
|
1104
|
+
BOND H N BOND CA N BOND C CA BOND O C
|
|
1105
|
+
BOND CB CA BOND CG CB BOND CD1 CG BOND CD2 CG
|
|
1106
|
+
BOND NE1 CD1 BOND CE2 CD2 BOND CE2 NE1 BOND CE3 CD2
|
|
1107
|
+
BOND CZ2 CE2 BOND CZ3 CE3 BOND CH2 CZ2 BOND CH2 CZ3
|
|
1108
|
+
BOND HD1 CD1 BOND HE1 NE1 BOND HE3 CE3 BOND HZ2 CZ2
|
|
1109
|
+
BOND HZ3 CZ3 BOND HH2 CH2
|
|
1110
|
+
|
|
1111
|
+
DIHEdral C CA N H
|
|
1112
|
+
DIHEdral O C CA N
|
|
1113
|
+
DIHEdral CB CA N H
|
|
1114
|
+
DIHEdral CB CA C O
|
|
1115
|
+
DIHEdral CG CB CA N MULT 3
|
|
1116
|
+
DIHEdral CG CB CA C MULT 3
|
|
1117
|
+
DIHEdral CD1 CG CB CA MULT 3
|
|
1118
|
+
DIHEdral CD2 CG CB CA MULT 3
|
|
1119
|
+
DIHEdral NE1 CD1 CG CB
|
|
1120
|
+
DIHEdral NE1 CD1 CG CD2
|
|
1121
|
+
DIHEdral CE2 CD2 CG CB
|
|
1122
|
+
DIHEdral CE2 CD2 CG CD1
|
|
1123
|
+
DIHEdral NE1 CE2 CD2 CG
|
|
1124
|
+
DIHEdral CE2 NE1 CD1 CG
|
|
1125
|
+
DIHEdral CD1 NE1 CE2 CD2
|
|
1126
|
+
DIHEdral CZ2 CE2 CD2 CG
|
|
1127
|
+
DIHEdral CZ2 CE2 NE1 CD1
|
|
1128
|
+
DIHEdral CE3 CD2 CG CB
|
|
1129
|
+
DIHEdral CE3 CD2 CG CD1
|
|
1130
|
+
DIHEdral CE3 CD2 CE2 NE1
|
|
1131
|
+
DIHEdral CE3 CD2 CE2 CZ2
|
|
1132
|
+
DIHEdral CZ3 CE3 CD2 CG
|
|
1133
|
+
DIHEdral CZ3 CE3 CD2 CE2
|
|
1134
|
+
DIHEdral CH2 CZ3 CE3 CD2
|
|
1135
|
+
DIHEdral CH2 CZ2 CE2 CD2
|
|
1136
|
+
DIHEdral CH2 CZ2 CE2 NE1
|
|
1137
|
+
DIHEdral CE2 CZ2 CH2 CZ3
|
|
1138
|
+
DIHEdral CZ2 CH2 CZ3 CE3
|
|
1139
|
+
DIHEdral HD1 CD1 CG CB
|
|
1140
|
+
DIHEdral HD1 CD1 CG CD2
|
|
1141
|
+
DIHEdral HD1 CD1 NE1 CE2
|
|
1142
|
+
DIHEdral HE1 NE1 CD1 HD1
|
|
1143
|
+
DIHEdral HE1 NE1 CD1 CG
|
|
1144
|
+
DIHEdral HE1 NE1 CE2 CD2
|
|
1145
|
+
DIHEdral HE1 NE1 CE2 CZ2
|
|
1146
|
+
DIHEdral HE3 CE3 CD2 CG
|
|
1147
|
+
DIHEdral HE3 CE3 CD2 CE2
|
|
1148
|
+
DIHEdral HE3 CE3 CZ3 CH2
|
|
1149
|
+
DIHEdral HZ2 CZ2 CE2 CD2
|
|
1150
|
+
DIHEdral HZ2 CZ2 CE2 NE1
|
|
1151
|
+
DIHEdral HZ2 CZ2 CH2 CZ3
|
|
1152
|
+
DIHEdral HZ3 CZ3 CE3 CD2
|
|
1153
|
+
DIHEdral HZ3 CZ3 CE3 HE3
|
|
1154
|
+
DIHEdral HZ3 CZ3 CH2 CZ2
|
|
1155
|
+
DIHEdral HH2 CH2 CZ2 CE2
|
|
1156
|
+
DIHEdral HH2 CH2 CZ2 HZ2
|
|
1157
|
+
DIHEdral HH2 CH2 CZ3 CE3
|
|
1158
|
+
DIHEdral HH2 CH2 CZ3 HZ3
|
|
1159
|
+
|
|
1160
|
+
IMPRoper CB CA N C
|
|
1161
|
+
IMProper CG NE1 CD1 HD1
|
|
1162
|
+
IMPRoper CD1 CE2 NE1 HE1
|
|
1163
|
+
IMPRoper CZ3 CD2 CE3 HE3
|
|
1164
|
+
IMPRoper CE2 CH2 CZ2 HZ2
|
|
1165
|
+
IMPRoper CH2 CE3 CZ3 HZ3
|
|
1166
|
+
IMPRoper CZ2 CZ3 CH2 HH2
|
|
1167
|
+
IMPRoper CD1 CG CD2 CB
|
|
1168
|
+
IMPRoper CE3 CD2 CG CE2
|
|
1169
|
+
IMPRoper CZ2 CE2 CD2 NE1
|
|
1170
|
+
|
|
1171
|
+
END
|
|
1172
|
+
! ==TRP==
|
|
1173
|
+
|
|
1174
|
+
! ========== END UNCAPPED AAs ==========
|
|
1175
|
+
|
|
1176
|
+
! ========== N-TERMINAL CAPS ==========
|
|
1177
|
+
! ========== SNAP-ON TOOLS ==========
|
|
1178
|
+
|
|
1179
|
+
! ==ACEG==
|
|
1180
|
+
PRESidue NAG
|
|
1181
|
+
ADD ATOM +C3 TYPE= C3 CHARge= 0.000 END
|
|
1182
|
+
ADD ATOM +CM TYPE= C CHARge= 0.500 END
|
|
1183
|
+
ADD ATOM +OM TYPE= O CHARge= -0.500 END
|
|
1184
|
+
|
|
1185
|
+
ADD BOND +C3 +CM
|
|
1186
|
+
ADD BOND +CM +OM
|
|
1187
|
+
ADD BOND +CM +N
|
|
1188
|
+
|
|
1189
|
+
ADD ANGLe +C3 +CM +OM
|
|
1190
|
+
ADD ANGLe +C3 +CM +N
|
|
1191
|
+
ADD ANGLe +OM +CM +N
|
|
1192
|
+
ADD ANGLe +CM +N +CA
|
|
1193
|
+
ADD ANGLe +CM +N +H
|
|
1194
|
+
|
|
1195
|
+
ADD DIHEdral +C3 +CM +N +CA MULT 2
|
|
1196
|
+
ADD DIHEdral +C3 +CM +N +H
|
|
1197
|
+
ADD DIHEdral +OM +CM +N +CA
|
|
1198
|
+
ADD DIHEdral +OM +CM +N +H
|
|
1199
|
+
ADD DIHEdral +CM +N +CA +C MULT 2
|
|
1200
|
+
|
|
1201
|
+
ADD IMPRoper +CM +N +C3 +OM
|
|
1202
|
+
ADD IMPRoper +N +CA +CM +H
|
|
1203
|
+
|
|
1204
|
+
END
|
|
1205
|
+
! ==ACEG==
|
|
1206
|
+
|
|
1207
|
+
! ==ACEX==
|
|
1208
|
+
PRESidue NAX
|
|
1209
|
+
ADD ATOM +C3 TYPE= C3 CHARge= 0.000 END
|
|
1210
|
+
ADD ATOM +CM TYPE= C CHARge= 0.500 END
|
|
1211
|
+
ADD ATOM +OM TYPE= O CHARge= -0.500 END
|
|
1212
|
+
|
|
1213
|
+
ADD BOND +C3 +CM
|
|
1214
|
+
ADD BOND +CM +OM
|
|
1215
|
+
ADD BOND +CM +N
|
|
1216
|
+
|
|
1217
|
+
ADD ANGLe +C3 +CM +OM
|
|
1218
|
+
ADD ANGLe +C3 +CM +N
|
|
1219
|
+
ADD ANGLe +OM +CM +N
|
|
1220
|
+
ADD ANGLe +CM +N +CA
|
|
1221
|
+
ADD ANGLe +CM +N +H
|
|
1222
|
+
|
|
1223
|
+
ADD DIHEdral +C3 +CM +N +CA MULT 2
|
|
1224
|
+
ADD DIHEdral +C3 +CM +N +H
|
|
1225
|
+
ADD DIHEdral +OM +CM +N +CA
|
|
1226
|
+
ADD DIHEdral +OM +CM +N +H
|
|
1227
|
+
ADD DIHEdral +CM +N +CA +C MULT 2
|
|
1228
|
+
ADD DIHEdral +CM +N +CA +CB MULT 2
|
|
1229
|
+
|
|
1230
|
+
ADD IMPRoper +CM +N +C3 +OM
|
|
1231
|
+
ADD IMPRoper +N +CA +CM +H
|
|
1232
|
+
|
|
1233
|
+
END
|
|
1234
|
+
! ==ACEX==
|
|
1235
|
+
|
|
1236
|
+
! =ACEP=
|
|
1237
|
+
PRESidue NAP
|
|
1238
|
+
ADD ATOM +C3 TYPE= C3 CHARge= 0.000 END
|
|
1239
|
+
ADD ATOM +CM TYPE= C CHARge= 0.500 END
|
|
1240
|
+
ADD ATOM +OM TYPE= O CHARge= -0.500 END
|
|
1241
|
+
|
|
1242
|
+
ADD BOND +C3 +CM
|
|
1243
|
+
ADD BOND +CM +OM
|
|
1244
|
+
ADD BOND +CM +N
|
|
1245
|
+
|
|
1246
|
+
ADD ANGLe +C3 +CM +OM
|
|
1247
|
+
ADD ANGLe +C3 +CM +N
|
|
1248
|
+
ADD ANGLe +OM +CM +N
|
|
1249
|
+
ADD ANGLe +CM +N +CA
|
|
1250
|
+
ADD ANGLe +CM +N +CD
|
|
1251
|
+
|
|
1252
|
+
ADD DIHEdral +C3 +CM +N +CA
|
|
1253
|
+
ADD DIHEdral +C3 +CM +N +CD
|
|
1254
|
+
ADD DIHEdral +OM +CM +N +CA
|
|
1255
|
+
ADD DIHEdral +OM +CM +N +CD
|
|
1256
|
+
ADD DIHEdral +CM +N +CA +C MULT 2
|
|
1257
|
+
ADD DIHEdral +CM +N +CA +CB MULT 2
|
|
1258
|
+
|
|
1259
|
+
ADD IMPRoper +CM +N +C3 +OM
|
|
1260
|
+
ADD IMPRoper +CM +CA +N +CD
|
|
1261
|
+
|
|
1262
|
+
END
|
|
1263
|
+
! =ACEP=
|
|
1264
|
+
! ========== END SNAP-ON TOOLS ==========
|
|
1265
|
+
|
|
1266
|
+
! ========== MODIFIED BACKBONE ==========
|
|
1267
|
+
|
|
1268
|
+
remarks N-TERMINAL PROTONATED AMINO GROUP NOT AVAILABLE FOR PROLINE
|
|
1269
|
+
remarks OR HYDROXYPROLINE - CAP INSTEAD
|
|
1270
|
+
|
|
1271
|
+
! =NGLYP=
|
|
1272
|
+
PRESidue GNP
|
|
1273
|
+
DELEte ATOM +H END
|
|
1274
|
+
MODIfy ATOM +N TYPE= N3 CHARge= -0.300 END
|
|
1275
|
+
MODIfy ATOM +CA TYPE= C2 CHARge= 0.310 END
|
|
1276
|
+
ADD ATOM +HT1 TYPE= H3 CHARge= 0.330 END
|
|
1277
|
+
ADD ATOM +HT2 TYPE= H3 CHARge= 0.330 END
|
|
1278
|
+
ADD ATOM +HT3 TYPE= H3 CHARge= 0.330 END
|
|
1279
|
+
|
|
1280
|
+
ADD BOND +HT1 +N
|
|
1281
|
+
ADD BOND +HT2 +N
|
|
1282
|
+
ADD BOND +HT3 +N
|
|
1283
|
+
|
|
1284
|
+
ADD ANGLe +HT2 +N +HT1
|
|
1285
|
+
ADD ANGLe +HT3 +N +HT1
|
|
1286
|
+
ADD ANGLe +HT3 +N +HT2
|
|
1287
|
+
ADD ANGLe +CA +N +HT1
|
|
1288
|
+
ADD ANGLe +CA +N +HT2
|
|
1289
|
+
ADD ANGLe +CA +N +HT3
|
|
1290
|
+
|
|
1291
|
+
ADD DIHEdral +C +CA +N +HT1
|
|
1292
|
+
ADD DIHEdral +C +CA +N +HT2
|
|
1293
|
+
ADD DIHEdral +C +CA +N +HT3
|
|
1294
|
+
|
|
1295
|
+
END
|
|
1296
|
+
! =NGLYP=
|
|
1297
|
+
|
|
1298
|
+
! =NXAAP=
|
|
1299
|
+
PRESidue XNP
|
|
1300
|
+
DELEte ATOM +H END
|
|
1301
|
+
MODIfy ATOM +N TYPE= N3 CHARge= -0.300 END
|
|
1302
|
+
MODIfy ATOM +CA TYPE= CH CHARge= 0.310 END
|
|
1303
|
+
ADD ATOM +HT1 TYPE= H3 CHARge= 0.330 END
|
|
1304
|
+
ADD ATOM +HT2 TYPE= H3 CHARge= 0.330 END
|
|
1305
|
+
ADD ATOM +HT3 TYPE= H3 CHARge= 0.330 END
|
|
1306
|
+
|
|
1307
|
+
ADD BOND +HT1 +N
|
|
1308
|
+
ADD BOND +HT2 +N
|
|
1309
|
+
ADD BOND +HT3 +N
|
|
1310
|
+
|
|
1311
|
+
ADD ANGLe +HT2 +N +HT1
|
|
1312
|
+
ADD ANGLe +HT3 +N +HT1
|
|
1313
|
+
ADD ANGLe +HT3 +N +HT2
|
|
1314
|
+
ADD ANGLe +CA +N +HT1
|
|
1315
|
+
ADD ANGLe +CA +N +HT2
|
|
1316
|
+
ADD ANGLe +CA +N +HT3
|
|
1317
|
+
|
|
1318
|
+
ADD DIHEdral +C +CA +N +HT1
|
|
1319
|
+
ADD DIHEdral +C +CA +N +HT2
|
|
1320
|
+
ADD DIHEdral +C +CA +N +HT3
|
|
1321
|
+
ADD DIHEdral +CB +CA +N +HT1
|
|
1322
|
+
ADD DIHEdral +CB +CA +N +HT2
|
|
1323
|
+
ADD DIHEdral +CB +CA +N +HT3
|
|
1324
|
+
|
|
1325
|
+
END
|
|
1326
|
+
! =NXAAP=
|
|
1327
|
+
|
|
1328
|
+
! ========== END MODIFIED BACKBONE ==========
|
|
1329
|
+
! ========== END N-TERMINAL CAPS ==========
|
|
1330
|
+
|
|
1331
|
+
! ========== C-TERMINAL CAPS ==========
|
|
1332
|
+
! ========== SNAP-ON TOOLS ==========
|
|
1333
|
+
|
|
1334
|
+
! ==NMEG==
|
|
1335
|
+
PRESIdue NMG
|
|
1336
|
+
ADD ATOM -NT TYPE= N CHARge= -0.570 END
|
|
1337
|
+
ADD ATOM -CT TYPE= C3b CHARge= 0.200 END
|
|
1338
|
+
ADD ATOM -HT TYPE= H CHARge= 0.370 END
|
|
1339
|
+
|
|
1340
|
+
ADD BOND -CT -NT
|
|
1341
|
+
ADD BOND -NT -HT
|
|
1342
|
+
ADD BOND -NT -C
|
|
1343
|
+
|
|
1344
|
+
ADD ANGLe -CT -NT -HT
|
|
1345
|
+
ADD ANGLe -CT -NT -C
|
|
1346
|
+
ADD ANGLe -HT -NT -C
|
|
1347
|
+
ADD ANGLe -NT -C -CA
|
|
1348
|
+
ADD ANGLe -NT -C -O
|
|
1349
|
+
|
|
1350
|
+
ADD DIHEdral -CT -NT -C -CA MULT 2
|
|
1351
|
+
ADD DIHEdral -CT -NT -C -O
|
|
1352
|
+
ADD DIHEdral -HT -NT -C -CA
|
|
1353
|
+
ADD DIHEdral -HT -NT -C -O
|
|
1354
|
+
ADD DIHEdral -NT -C -CA -N MULT 2
|
|
1355
|
+
|
|
1356
|
+
ADD IMPRoper -NT -CT -C -HT
|
|
1357
|
+
ADD IMPRoper -C -NT -CA -O
|
|
1358
|
+
|
|
1359
|
+
END
|
|
1360
|
+
! ==NMEG==
|
|
1361
|
+
|
|
1362
|
+
! ==NMEX==
|
|
1363
|
+
PRESIdue NMX
|
|
1364
|
+
ADD ATOM -NT TYPE= N CHARge= -0.570 END
|
|
1365
|
+
ADD ATOM -CT TYPE= C3b CHARge= 0.200 END
|
|
1366
|
+
ADD ATOM -HT TYPE= H CHARge= 0.370 END
|
|
1367
|
+
|
|
1368
|
+
ADD BOND -CT -NT
|
|
1369
|
+
ADD BOND -NT -HT
|
|
1370
|
+
ADD BOND -NT -C
|
|
1371
|
+
|
|
1372
|
+
ADD ANGLe -CT -NT -HT
|
|
1373
|
+
ADD ANGLe -CT -NT -C
|
|
1374
|
+
ADD ANGLe -HT -NT -C
|
|
1375
|
+
ADD ANGLe -NT -C -CA
|
|
1376
|
+
ADD ANGLe -NT -C -O
|
|
1377
|
+
|
|
1378
|
+
ADD DIHEdral -CT -NT -C -CA MULT 2
|
|
1379
|
+
ADD DIHEdral -CT -NT -C -O
|
|
1380
|
+
ADD DIHEdral -HT -NT -C -CA
|
|
1381
|
+
ADD DIHEdral -HT -NT -C -O
|
|
1382
|
+
ADD DIHEdral -NT -C -CA -N MULT 2
|
|
1383
|
+
ADD DIHEdral -NT -C -CA -CB MULT 3
|
|
1384
|
+
|
|
1385
|
+
ADD IMPRoper -NT -CT -C -HT
|
|
1386
|
+
ADD IMPRoper -C -NT -CA -O
|
|
1387
|
+
|
|
1388
|
+
END
|
|
1389
|
+
! ==NMEG==
|
|
1390
|
+
|
|
1391
|
+
! ==NH2G==
|
|
1392
|
+
PRESIdue AMG
|
|
1393
|
+
ADD ATOM -NT TYPE= N CHARge= -0.850 END
|
|
1394
|
+
ADD ATOM -HT1 TYPE= Ha CHARge= 0.425 END
|
|
1395
|
+
ADD ATOM -HT2 TYPE= Ha CHARge= 0.425 END
|
|
1396
|
+
|
|
1397
|
+
ADD BOND -HT1 -NT
|
|
1398
|
+
ADD BOND -HT2 -NT
|
|
1399
|
+
ADD BOND -NT -C
|
|
1400
|
+
|
|
1401
|
+
ADD ANGLe -HT1 -NT -HT2
|
|
1402
|
+
ADD ANGLe -HT1 -NT -C
|
|
1403
|
+
ADD ANGLe -HT2 -NT -C
|
|
1404
|
+
ADD ANGLe -NT -C -CA
|
|
1405
|
+
ADD ANGLe -NT -C -O
|
|
1406
|
+
|
|
1407
|
+
ADD DIHEdral -HT1 -NT -C -CA
|
|
1408
|
+
ADD DIHEdral -HT1 -NT -C -O
|
|
1409
|
+
ADD DIHEdral -HT2 -NT -C -CA
|
|
1410
|
+
ADD DIHEdral -HT2 -NT -C -O
|
|
1411
|
+
ADD DIHEdral -NT -C -CA -N MULT 2
|
|
1412
|
+
|
|
1413
|
+
ADD IMPRoper -C -HT1 -NT -HT2
|
|
1414
|
+
ADD IMPRoper -C -NT -CA -O
|
|
1415
|
+
|
|
1416
|
+
END
|
|
1417
|
+
! ==NH2G==
|
|
1418
|
+
|
|
1419
|
+
! ==NH2X==
|
|
1420
|
+
PRESIdue AMX
|
|
1421
|
+
ADD ATOM -NT TYPE= N CHARge= -0.850 END
|
|
1422
|
+
ADD ATOM -HT1 TYPE= Ha CHARge= 0.425 END
|
|
1423
|
+
ADD ATOM -HT2 TYPE= Ha CHARge= 0.425 END
|
|
1424
|
+
|
|
1425
|
+
ADD BOND -HT1 -NT
|
|
1426
|
+
ADD BOND -HT2 -NT
|
|
1427
|
+
ADD BOND -NT -C
|
|
1428
|
+
|
|
1429
|
+
ADD ANGLe -HT1 -NT -HT2
|
|
1430
|
+
ADD ANGLe -HT1 -NT -C
|
|
1431
|
+
ADD ANGLe -HT2 -NT -C
|
|
1432
|
+
ADD ANGLe -NT -C -CA
|
|
1433
|
+
ADD ANGLe -NT -C -O
|
|
1434
|
+
|
|
1435
|
+
ADD DIHEdral -HT1 -NT -C -CA
|
|
1436
|
+
ADD DIHEdral -HT1 -NT -C -O
|
|
1437
|
+
ADD DIHEdral -HT2 -NT -C -CA
|
|
1438
|
+
ADD DIHEdral -HT2 -NT -C -O
|
|
1439
|
+
ADD DIHEdral -NT -C -CA -N MULT 2
|
|
1440
|
+
ADD DIHEdral -NT -C -CA -CB MULT 3
|
|
1441
|
+
|
|
1442
|
+
ADD IMPRoper -C -HT1 -NT -HT2
|
|
1443
|
+
ADD IMPRoper -C -NT -CA -O
|
|
1444
|
+
|
|
1445
|
+
END
|
|
1446
|
+
! ==NH2X==
|
|
1447
|
+
|
|
1448
|
+
! ========== END SNAP-ON TOOLS ==========
|
|
1449
|
+
|
|
1450
|
+
! ========== MODIFIED BACKBONE ==========
|
|
1451
|
+
|
|
1452
|
+
! =CGLYM=
|
|
1453
|
+
PRESidue GCM
|
|
1454
|
+
DELEte ATOM -O END
|
|
1455
|
+
MODIfy ATOM -CA TYPE= C2 CHARge= 0.100 END
|
|
1456
|
+
MODIfy ATOM -C TYPE= C CHARge= 0.700 END
|
|
1457
|
+
ADD ATOM -OT1 TYPE= O2 CHARge= -0.800 END
|
|
1458
|
+
ADD ATOM -OT2 TYPE= O2 CHARge= -0.800 END
|
|
1459
|
+
|
|
1460
|
+
ADD BOND -OT1 -C
|
|
1461
|
+
ADD BOND -OT2 -C
|
|
1462
|
+
|
|
1463
|
+
ADD ANGLe -OT1 -C -CA
|
|
1464
|
+
ADD ANGLe -OT2 -C -CA
|
|
1465
|
+
ADD ANGLe -OT2 -C -OT1
|
|
1466
|
+
|
|
1467
|
+
ADD DIHEdral -OT1 -C -CA -N
|
|
1468
|
+
ADD DIHEdral -OT2 -C -CA -N
|
|
1469
|
+
|
|
1470
|
+
ADD IMPRoper -CA -OT1 -C -OT2
|
|
1471
|
+
|
|
1472
|
+
END
|
|
1473
|
+
! =CGLYM=
|
|
1474
|
+
|
|
1475
|
+
! =CXAAM=
|
|
1476
|
+
PRESidue XCM
|
|
1477
|
+
DELEte ATOM -O END
|
|
1478
|
+
MODIfY ATOM -CA TYPE= CH CHARge= 0.100 END
|
|
1479
|
+
MODIfy ATOM -C TYPE= C CHARge= 0.700 END
|
|
1480
|
+
ADD ATOM -OT1 TYPE= O2 CHARge= -0.800 END
|
|
1481
|
+
ADD ATOM -OT2 TYPE= O2 CHARge= -0.800 END
|
|
1482
|
+
|
|
1483
|
+
ADD BOND -OT1 -C
|
|
1484
|
+
ADD BOND -OT2 -C
|
|
1485
|
+
|
|
1486
|
+
ADD ANGLe -OT1 -C -CA
|
|
1487
|
+
ADD ANGLe -OT2 -C -CA
|
|
1488
|
+
ADD ANGLe -OT2 -C -OT1
|
|
1489
|
+
|
|
1490
|
+
ADD DIHEdral -OT1 -C -CA -N
|
|
1491
|
+
ADD DIHEdral -OT2 -C -CA -N
|
|
1492
|
+
ADD DIHEdral -OT1 -C -CA -CB
|
|
1493
|
+
ADD DIHEdral -OT2 -C -CA -CB
|
|
1494
|
+
|
|
1495
|
+
ADD IMPRoper -CA -OT1 -C -OT2
|
|
1496
|
+
|
|
1497
|
+
END
|
|
1498
|
+
! =CXAAM=
|
|
1499
|
+
|
|
1500
|
+
remarks TORSIONS FOR C-TERMINAL ESTER NOT AVAILABLE - CHOOSE OTHER CAP
|
|
1501
|
+
|
|
1502
|
+
! =COMEG=
|
|
1503
|
+
PRESidue GOM
|
|
1504
|
+
MODIfy ATOM -CA TYPE= C2 CHARge= 0.250 END
|
|
1505
|
+
MODIfy ATOM -C TYPE= C CHARge= 0.550 END
|
|
1506
|
+
MODIfy ATOM -O TYPE= O CHARge= -0.450 END
|
|
1507
|
+
ADD ATOM -OT TYPE= OS CHARge= -0.400 END
|
|
1508
|
+
ADD ATOM -CT TYPE= C3b CHARge= 0.250 END
|
|
1509
|
+
|
|
1510
|
+
ADD BOND -OT -C
|
|
1511
|
+
ADD BOND -CT -OT
|
|
1512
|
+
|
|
1513
|
+
ADD ANGLe -OT -C -CA
|
|
1514
|
+
ADD ANGLe -OT -C -O
|
|
1515
|
+
ADD ANGLe -CT -OT -C
|
|
1516
|
+
|
|
1517
|
+
ADD DIHEdral -OT -C -CA -N
|
|
1518
|
+
ADD DIHEdral -CT -OT -C -CA
|
|
1519
|
+
ADD DIHEdral -CT -OT -C -O
|
|
1520
|
+
|
|
1521
|
+
ADD IMPRoper -CA -OT -C -O
|
|
1522
|
+
|
|
1523
|
+
END
|
|
1524
|
+
! =COMEG=
|
|
1525
|
+
|
|
1526
|
+
! =COMEX=
|
|
1527
|
+
PRESidue XOM
|
|
1528
|
+
MODIfy ATOM -CA TYPE= CH CHARge= 0.250 END
|
|
1529
|
+
MODIfy ATOM -C TYPE= C CHARge= 0.550 END
|
|
1530
|
+
MODIfy ATOM -O TYPE= O CHARge= -0.450 END
|
|
1531
|
+
ADD ATOM -OT TYPE= OS CHARge= -0.400 END
|
|
1532
|
+
ADD ATOM -CT TYPE= C3b CHARge= 0.250 END
|
|
1533
|
+
|
|
1534
|
+
ADD BOND -OT -C
|
|
1535
|
+
ADD BOND -CT -OT
|
|
1536
|
+
|
|
1537
|
+
ADD ANGLe -OT -C -CA
|
|
1538
|
+
ADD ANGLe -OT -C -O
|
|
1539
|
+
ADD ANGLe -CT -OT -C
|
|
1540
|
+
|
|
1541
|
+
ADD DIHEdral -OT -C -CA -N
|
|
1542
|
+
ADD DIHEdral -OT -C -CA -CB
|
|
1543
|
+
ADD DIHEdral -CT -OT -C -CA
|
|
1544
|
+
ADD DIHEdral -CT -OT -C -O
|
|
1545
|
+
|
|
1546
|
+
ADD IMPRoper -CA -OT -C -O
|
|
1547
|
+
|
|
1548
|
+
END
|
|
1549
|
+
! =COMEX=
|
|
1550
|
+
|
|
1551
|
+
! ========== END MODIFIED BACKBONE ==========
|
|
1552
|
+
! ========== END C-TERMINAL CAPS ==========
|
|
1553
|
+
! ========== END RESIDUE CONSTRUCTION ==========
|
|
1554
|
+
|
|
1555
|
+
! ========== RESIDUE LINKING ==========
|
|
1556
|
+
|
|
1557
|
+
! ========== MIDDLE RESIDUE LINKING ==========
|
|
1558
|
+
|
|
1559
|
+
! =GPEPG=
|
|
1560
|
+
PRESidue GMG
|
|
1561
|
+
ADD BOND -C +N
|
|
1562
|
+
|
|
1563
|
+
ADD ANGLe -CA -C +N
|
|
1564
|
+
ADD ANGLe -O -C +N
|
|
1565
|
+
ADD ANGLe -C +N +CA
|
|
1566
|
+
ADD ANGLe -C +N +H
|
|
1567
|
+
|
|
1568
|
+
ADD DIHEdral -N -CA -C +N MULT 2
|
|
1569
|
+
ADD DIHEdral -CA -C +N +CA MULT 2
|
|
1570
|
+
ADD DIHEdral -CA -C +N +H
|
|
1571
|
+
ADD DIHEdral -O -C +N +CA
|
|
1572
|
+
ADD DIHEdral -O -C +N +H
|
|
1573
|
+
ADD DIHEdral -C +N +CA +C MULT 2
|
|
1574
|
+
|
|
1575
|
+
ADD IMPRoper -C +N -CA -O
|
|
1576
|
+
ADD IMPRoper +N +CA -C +H
|
|
1577
|
+
|
|
1578
|
+
END
|
|
1579
|
+
! =GPEPG=
|
|
1580
|
+
|
|
1581
|
+
! =XPEPG=
|
|
1582
|
+
PRESidue XMG
|
|
1583
|
+
ADD BOND -C +N
|
|
1584
|
+
|
|
1585
|
+
ADD ANGLe -CA -C +N
|
|
1586
|
+
ADD ANGLe -O -C +N
|
|
1587
|
+
ADD ANGLe -C +N +CA
|
|
1588
|
+
ADD ANGLe -C +N +H
|
|
1589
|
+
|
|
1590
|
+
ADD DIHEdral -N -CA -C +N MULT 2
|
|
1591
|
+
ADD DIHEdral -CB -CA -C +N MULT 3
|
|
1592
|
+
ADD DIHEdral -CA -C +N +CA MULT 2
|
|
1593
|
+
ADD DIHEdral -CA -C +N +H
|
|
1594
|
+
ADD DIHEdral -O -C +N +CA
|
|
1595
|
+
ADD DIHEdral -O -C +N +H
|
|
1596
|
+
ADD DIHEdral -C +N +CA +C MULT 2
|
|
1597
|
+
|
|
1598
|
+
ADD IMPRoper -C +N -CA -O
|
|
1599
|
+
ADD IMPRoper +N +CA -C +H
|
|
1600
|
+
|
|
1601
|
+
END
|
|
1602
|
+
! =XPEPG=
|
|
1603
|
+
|
|
1604
|
+
! =GPEPX=
|
|
1605
|
+
PRESidue GMX
|
|
1606
|
+
ADD BOND -C +N
|
|
1607
|
+
|
|
1608
|
+
ADD ANGLe -CA -C +N
|
|
1609
|
+
ADD ANGLe -O -C +N
|
|
1610
|
+
ADD ANGLe -C +N +CA
|
|
1611
|
+
ADD ANGLe -C +N +H
|
|
1612
|
+
|
|
1613
|
+
ADD DIHEdral -N -CA -C +N MULT 2
|
|
1614
|
+
ADD DIHEdral -CA -C +N +CA MULT 2
|
|
1615
|
+
ADD DIHEdral -CA -C +N +H
|
|
1616
|
+
ADD DIHEdral -O -C +N +CA
|
|
1617
|
+
ADD DIHEdral -O -C +N +H
|
|
1618
|
+
ADD DIHEdral -C +N +CA +C MULT 2
|
|
1619
|
+
ADD DIHEdral -C +N +CA +CB MULT 2
|
|
1620
|
+
|
|
1621
|
+
ADD IMPRoper -C +N -CA -O
|
|
1622
|
+
ADD IMPRoper +N +CA -C +H
|
|
1623
|
+
|
|
1624
|
+
END
|
|
1625
|
+
! =GPEPX=
|
|
1626
|
+
|
|
1627
|
+
! =XPEPX=
|
|
1628
|
+
PRESidue XMX
|
|
1629
|
+
ADD BOND -C +N
|
|
1630
|
+
|
|
1631
|
+
ADD ANGLe -CA -C +N
|
|
1632
|
+
ADD ANGLe -O -C +N
|
|
1633
|
+
ADD ANGLe -C +N +CA
|
|
1634
|
+
ADD ANGLe -C +N +H
|
|
1635
|
+
|
|
1636
|
+
ADD DIHEdral -N -CA -C +N MULT 2
|
|
1637
|
+
ADD DIHEdral -CB -CA -C +N MULT 3
|
|
1638
|
+
ADD DIHEdral -CA -C +N +CA MULT 2
|
|
1639
|
+
ADD DIHEdral -CA -C +N +H
|
|
1640
|
+
ADD DIHEdral -O -C +N +CA
|
|
1641
|
+
ADD DIHEdral -O -C +N +H
|
|
1642
|
+
ADD DIHEdral -C +N +CA +C MULT 2
|
|
1643
|
+
ADD DIHEdral -C +N +CA +CB MULT 2
|
|
1644
|
+
|
|
1645
|
+
ADD IMPRoper -C +N -CA -O
|
|
1646
|
+
ADD IMPRoper +N +CA -C +H
|
|
1647
|
+
|
|
1648
|
+
END
|
|
1649
|
+
! =XPEPX=
|
|
1650
|
+
|
|
1651
|
+
! =GPEPP=
|
|
1652
|
+
PRESidue GMP
|
|
1653
|
+
ADD BOND -C +N
|
|
1654
|
+
|
|
1655
|
+
ADD ANGLE -CA -C +N
|
|
1656
|
+
ADD ANGLE -O -C +N
|
|
1657
|
+
ADD ANGLE -C +N +CA
|
|
1658
|
+
ADD ANGLE -C +N +CD
|
|
1659
|
+
|
|
1660
|
+
ADD DIHEdral -N -CA -C +N MULT 2
|
|
1661
|
+
ADD DIHEdral -CA -C +N +CA
|
|
1662
|
+
ADD DIHEdral -CA -C +N +CD
|
|
1663
|
+
ADD DIHEdral -O -C +N +CD
|
|
1664
|
+
ADD DIHEdral -O -C +N +CA
|
|
1665
|
+
ADD DIHEdral -C +N +CA +C MULT 2
|
|
1666
|
+
ADD DIHEdral -C +N +CA +CB MULT 2
|
|
1667
|
+
ADD DIHEdral -C +N +CD +CG MULT 3
|
|
1668
|
+
|
|
1669
|
+
|
|
1670
|
+
ADD IMPRoper -C +N -CA -O
|
|
1671
|
+
ADD IMPRoper -C +CA +N +CD
|
|
1672
|
+
|
|
1673
|
+
END
|
|
1674
|
+
! =GPEPP=
|
|
1675
|
+
|
|
1676
|
+
! =XPEPP=
|
|
1677
|
+
PRESidue XMP
|
|
1678
|
+
ADD BOND -C +N
|
|
1679
|
+
|
|
1680
|
+
ADD ANGLE -CA -C +N
|
|
1681
|
+
ADD ANGLE -O -C +N
|
|
1682
|
+
ADD ANGLE -C +N +CA
|
|
1683
|
+
ADD ANGLE -C +N +CD
|
|
1684
|
+
|
|
1685
|
+
ADD DIHEdral -N -CA -C +N MULT 2
|
|
1686
|
+
ADD DIHEdral -CB -CA -C +N MULT 3
|
|
1687
|
+
ADD DIHEdral -CA -C +N +CA
|
|
1688
|
+
ADD DIHEdral -CA -C +N +CD
|
|
1689
|
+
ADD DIHEdral -O -C +N +CD
|
|
1690
|
+
ADD DIHEdral -O -C +N +CA
|
|
1691
|
+
ADD DIHEdral -C +N +CA +C MULT 2
|
|
1692
|
+
ADD DIHEdral -C +N +CA +CB MULT 2
|
|
1693
|
+
ADD DIHEdral -C +N +CD +CG MULT 3
|
|
1694
|
+
|
|
1695
|
+
|
|
1696
|
+
ADD IMPRoper -C +N -CA -O
|
|
1697
|
+
ADD IMPRoper -C +CA +N +CD
|
|
1698
|
+
|
|
1699
|
+
END
|
|
1700
|
+
! =XPEPP=
|
|
1701
|
+
|
|
1702
|
+
! =S---S=
|
|
1703
|
+
|
|
1704
|
+
remarks USE CYT - NOT CYS - FOR CYS INVOLVED IN DISULFIDE BRIDGES
|
|
1705
|
+
remarks TORSIONS NEED TO BE REFIT - EXISTING ONES ARE TEMPORARY
|
|
1706
|
+
|
|
1707
|
+
PRESidue DISU
|
|
1708
|
+
ADD BOND 1SG 2SG
|
|
1709
|
+
|
|
1710
|
+
ADD ANGLe 1CB 1SG 2SG
|
|
1711
|
+
ADD ANGLe 1SG 2SG 2CB
|
|
1712
|
+
|
|
1713
|
+
ADD DIHEdral 1CA 1CB 1SG 2SG
|
|
1714
|
+
ADD DIHEdral 1CB 1SG 2SG 2CB
|
|
1715
|
+
ADD DIHEdral 1SG 2SG 2CB 2CA
|
|
1716
|
+
|
|
1717
|
+
END
|
|
1718
|
+
! =S---S=
|
|
1719
|
+
|
|
1720
|
+
! ========== END MIDDLE RESIDUE LINKING ==========
|
|
1721
|
+
! ========== END RESIDUE LINKING ==========
|
|
1722
|
+
|
|
1723
|
+
! ========== ADDITIONAL GOODIES ==========
|
|
1724
|
+
! ========== POPULAR SOLVENTS ==========
|
|
1725
|
+
|
|
1726
|
+
! =TIP3P=
|
|
1727
|
+
RESIdue WAT
|
|
1728
|
+
GROUp
|
|
1729
|
+
ATOM OH2 TYPE= OW CHARge= -0.834 END
|
|
1730
|
+
ATOM H1 TYPE= HW CHARge= 0.417 END
|
|
1731
|
+
ATOM H2 TYPE= HW CHARge= 0.417 END
|
|
1732
|
+
|
|
1733
|
+
BOND H1 OH2 BOND H2 OH2 BOND H2 H1
|
|
1734
|
+
|
|
1735
|
+
END
|
|
1736
|
+
! =TIP3P=
|
|
1737
|
+
|
|
1738
|
+
! =UREA==
|
|
1739
|
+
RESIdue URE
|
|
1740
|
+
GROUp
|
|
1741
|
+
ATOM C TYPE= C1 CHARge= 0.142 END
|
|
1742
|
+
ATOM O TYPE= O CHARge= -0.390 END
|
|
1743
|
+
ATOM N1 TYPE= N CHARge= -0.542 END
|
|
1744
|
+
ATOM N2 TYPE= N CHARge= -0.542 END
|
|
1745
|
+
ATOM H11 TYPE= Ha CHARge= 0.333 END
|
|
1746
|
+
ATOM H12 TYPE= Ha CHARge= 0.333 END
|
|
1747
|
+
ATOM H21 TYPE= Ha CHARge= 0.333 END
|
|
1748
|
+
ATOM H22 TYPE= Ha CHARge= 0.333 END
|
|
1749
|
+
|
|
1750
|
+
BOND O C BOND N1 C BOND N2 C
|
|
1751
|
+
BOND H11 N1 BOND H12 N1 BOND H21 N2 BOND H22 N2
|
|
1752
|
+
|
|
1753
|
+
DIHEdral H11 N1 C N2
|
|
1754
|
+
DIHEdral H11 N1 C O
|
|
1755
|
+
DIHEdral H12 N1 C N2
|
|
1756
|
+
DIHEdral H12 N1 C O
|
|
1757
|
+
DIHEdral H21 N2 C N1
|
|
1758
|
+
DIHEdral H21 N2 C O
|
|
1759
|
+
DIHEdral H22 N2 C N1
|
|
1760
|
+
DIHEdral H22 N2 C O
|
|
1761
|
+
|
|
1762
|
+
IMPRoper C N2 N1 O
|
|
1763
|
+
IMPRoper C H11 N1 H12
|
|
1764
|
+
IMPRoper C H21 N2 H22
|
|
1765
|
+
|
|
1766
|
+
END
|
|
1767
|
+
! =UREA==
|
|
1768
|
+
|
|
1769
|
+
! ==TFE==
|
|
1770
|
+
RESIdue TFE
|
|
1771
|
+
GROUp
|
|
1772
|
+
ATOM CF3 TYPE= CTf CHARge= 0.5323 END
|
|
1773
|
+
ATOM CH2 TYPE= CT CHARge= 0.1263 END
|
|
1774
|
+
ATOM OH TYPE= OH CHARge= -0.6351 END
|
|
1775
|
+
ATOM HO TYPE= HO CHARge= 0.4286 END
|
|
1776
|
+
ATOM FC1 TYPE= F CHARge= -0.2057 END
|
|
1777
|
+
ATOM FC2 TYPE= F CHARge= -0.2057 END
|
|
1778
|
+
ATOM FC3 TYPE= F CHARge= -0.2057 END
|
|
1779
|
+
ATOM HC1 TYPE= HCa CHARge= 0.0825 END
|
|
1780
|
+
ATOM HC2 TYPE= HCa CHARge= 0.0825 END
|
|
1781
|
+
|
|
1782
|
+
BOND CH2 CF3 BOND OH CH2 BOND HO OH
|
|
1783
|
+
BOND FC1 CF3 BOND FC2 CF3 BOND FC3 CF3
|
|
1784
|
+
BOND HC1 CH2 BOND HC2 CH2
|
|
1785
|
+
|
|
1786
|
+
DIHEdral CF3 CH2 OH HO MULT 2
|
|
1787
|
+
DIHEdral FC1 CF3 CH2 OH
|
|
1788
|
+
DIHEdral FC2 CF3 CH2 OH
|
|
1789
|
+
DIHEdral FC3 CF3 CH2 OH
|
|
1790
|
+
DIHEdral HC1 CH2 OH HO
|
|
1791
|
+
DIHEdral HC1 CH2 CF3 FC1
|
|
1792
|
+
DIHEdral HC1 CH2 CF3 FC2
|
|
1793
|
+
DIHEdral HC1 CH2 CF3 FC3
|
|
1794
|
+
DIHEdral HC2 CH2 OH HO
|
|
1795
|
+
DIHEdral HC2 CH2 CF3 FC1
|
|
1796
|
+
DIHEdral HC2 CH2 CF3 FC2
|
|
1797
|
+
DIHEdral HC2 CH2 CF3 FC3
|
|
1798
|
+
|
|
1799
|
+
END
|
|
1800
|
+
! ==TFE==
|
|
1801
|
+
|
|
1802
|
+
! ========== END POPULAR SOLVENTS ==========
|
|
1803
|
+
|
|
1804
|
+
! ========== COUNTERIONS, ETC ==========
|
|
1805
|
+
|
|
1806
|
+
! ==SOD==
|
|
1807
|
+
RESIdue SOD
|
|
1808
|
+
GROUp
|
|
1809
|
+
ATOM Na TYPE= SOD CHARge= 1.000 END
|
|
1810
|
+
|
|
1811
|
+
END
|
|
1812
|
+
! ==SOD==
|
|
1813
|
+
|
|
1814
|
+
! ==CHL==
|
|
1815
|
+
RESIdue CHL
|
|
1816
|
+
GROUp
|
|
1817
|
+
ATOM Cl TYPE= CHL CHARge= -1.000 END
|
|
1818
|
+
|
|
1819
|
+
END
|
|
1820
|
+
! ==CHL==
|
|
1821
|
+
|
|
1822
|
+
! ==NH4==
|
|
1823
|
+
RESIdue NH4
|
|
1824
|
+
GROUp
|
|
1825
|
+
ATOM N TYPE= N3 CHARge= -0.400 END
|
|
1826
|
+
ATOM H1 TYPE= H3 CHARge= 0.350 END
|
|
1827
|
+
ATOM H2 TYPE= H3 CHARge= 0.350 END
|
|
1828
|
+
ATOM H3 TYPE= H3 CHARge= 0.350 END
|
|
1829
|
+
ATOM H4 TYPE= H3 CHARge= 0.350 END
|
|
1830
|
+
|
|
1831
|
+
BOND H1 N BOND H2 N BOND H3 N BOND H4 N
|
|
1832
|
+
|
|
1833
|
+
END
|
|
1834
|
+
! ==NH4==
|
|
1835
|
+
|
|
1836
|
+
! ==SO4==
|
|
1837
|
+
RESIdue SO4
|
|
1838
|
+
GROUp
|
|
1839
|
+
ATOM S TYPE= S CHARge= -2.000 END
|
|
1840
|
+
ATOM O1 TYPE= O4 CHARge= 1.000 END
|
|
1841
|
+
ATOM O2 TYPE= O4 CHARge= 1.000 END
|
|
1842
|
+
ATOM O3 TYPE= O4 CHARge= 1.000 END
|
|
1843
|
+
ATOM O4 TYPE= O4 CHARge= 1.000 END
|
|
1844
|
+
|
|
1845
|
+
BOND O1 S BOND O2 S BOND O3 S BOND O4 S
|
|
1846
|
+
|
|
1847
|
+
END
|
|
1848
|
+
! ==SO4==
|
|
1849
|
+
|
|
1850
|
+
! ==CA2==
|
|
1851
|
+
RESIdue CA2
|
|
1852
|
+
GROUp
|
|
1853
|
+
ATOM CAL TYPE= CAL CHARge= 2.000 END
|
|
1854
|
+
|
|
1855
|
+
END
|
|
1856
|
+
! ==CA2==
|
|
1857
|
+
|
|
1858
|
+
! ==YB3==
|
|
1859
|
+
RESIdue YB3
|
|
1860
|
+
GROUp
|
|
1861
|
+
ATOM YB TYPE= YB CHARge= 2.000 END
|
|
1862
|
+
|
|
1863
|
+
END
|
|
1864
|
+
! ==YB3==
|
|
1865
|
+
|
|
1866
|
+
! ========== END COUNTERIONS, ETC ==========
|
|
1867
|
+
! ========== MORE GOODIES TO COME ==========
|
|
1868
|
+
|
|
1869
|
+
set echo=false end
|