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par_all27_prot_lipid.prm
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par_all27_prot_lipid.prm
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*>CHARMM22 All-Hydrogen Parameter File for Proteins and Lipids <<
*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
*>>>>>>>>>>>>>>>>>>>>>> July, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
* All comments to ADM jr. via the CHARMM web site: www.charmm.org
* parameter set discussion forum
*
! references
!
!PROTEINS
!
!MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, Extending the
!treatment of backbone energetics in protein force fields: limitations
!of gas-phase quantum mechanics in reproducing protein conformational
!distributions in molecular dynamics simulations, Journal of
!Computational Chemistry, 25: 1400-1415, 2004.
!
!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.;
!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.;
!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos,
!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III,
!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.;
!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom
!empirical potential for molecular modeling and dynamics Studies of
!proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616.
!
!ZINC
!
!Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and
!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS:
!Structure, Function, and Genetics 23:12-31 (1995)
!
!LIPIDS
!
!Feller, S.E. Gawrisch, G. and MacKerell, Jr., A.D. Polyunsaturated
!Fatty Acids in Lipid Bilayers: Intrinsic and Environmental
!Contributions to Their Unique Physical Properties. Journal of
!the American Chemical Society, 2002, 124:318-326
!
!Feller, S. and MacKerell, Jr., A.D. An Improved Empirical Potential
!Energy Function for Molecular Simulations of Phospholipids, Journal
!of Physical Chemistry B, 2000, 104: 7510-7515.
!
!and
!
!Schlenkrich, M., Brickmann, J., MacKerell, Jr., A.D., and Karplus, M.
!Empirical Potential Energy Function for Phospholipids: Criteria for
!Parameter Optimization and Applications, in "Biological Membranes: A
!Molecular Perspective from Computation and Experiment," K.M. Merz and
!B. Roux, Eds. Birkhauser, Boston, 1996, pp 31-81.
!
!new ALKANES
!
!Yin, D. and MacKerell, Jr. A.D. Combined Ab initio/Empirical Approach
!for the Optimization of Lennard-Jones Parameters. Journal of
!Computational Chemistry, 1998, 19: 334-338.
!
!ALKENES
!
!Feller, S.E., Yin, D., Pastor, R.W., and MacKerell, Jr., A.D.,
!Molecular Dynamics Simulation of Unsaturated Lipids at Low Hydration:
!Parameterization and Comparison with Diffraction Studies. Biophysical
!Journal, 73:2269-2279, 1997.
!
!new PHOSPHATE
!
!MacKerell, Jr., A.D. Influence of Water and Sodium on the Energetics
!of Dimethylphosphate and its Implications For DNA Structure, Journal
!de Chimie Physique, 1997, 94: 1436-1447.
!
!IONS
!
!all ions from Roux and coworkers
!
!Sodium
!
!Beglov, D. and Roux, B., Finite Representation of an Infinite
!Bulk System: Solvent Boundary Potential for Computer Simulations,
!Journal of Chemical Physics, 1994, 100: 9050-9063
!
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
!Carbon Dioxide
CST OST 937.96 1.1600 ! JES
!Heme to Sulfate (PSUL) link
SS FE 250.0 2.3200 !force constant a guess
!equilbrium bond length optimized to reproduce
!CSD survey values of
!2.341pm0.01 (mean, standard error)
!adm jr., 7/01
C C 600.000 1.3350 ! ALLOW ARO HEM
! Heme vinyl substituent (KK, from propene (JCS))
CA CA 305.000 1.3750 ! ALLOW ARO
! benzene, JES 8/25/89
CE1 CE1 440.000 1.3400 !
! for butene; from propene, yin/adm jr., 12/95
CE1 CE2 500.000 1.3420 !
! for propene, yin/adm jr., 12/95
CE1 CT2 365.000 1.5020 !
! for butene; from propene, yin/adm jr., 12/95
CE1 CT3 383.000 1.5040 !
! for butene, yin/adm jr., 12/95
CE2 CE2 510.000 1.3300 !
! for ethene, yin/adm jr., 12/95
CP1 C 250.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP1 CC 250.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP1 CD 200.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 222.500 1.5270 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP2 222.500 1.5370 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 CP2 222.500 1.5370 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CPB CE1 450.000 1.3800 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CPB CPA 299.800 1.4432 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB CPB 340.700 1.3464 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPH1 CPH1 410.000 1.3600 ! ALLOW ARO
! histidine, adm jr., 6/27/90
CPM CPA 360.000 1.3716 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPT CA 305.000 1.3680 ! ALLOW ARO
! adm jr., 12/30/91, for jwk
CPT CPT 360.000 1.4000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT1 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT1 CT1 222.500 1.5000 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT2 CA 230.000 1.4900 ! ALLOW ALI ARO
! phe,tyr, JES 8/25/89
CT2 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT2 CPB 230.000 1.4900 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT2 CPH1 229.630 1.5000 ! ALLOW ARO
! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
CT2 CT1 222.500 1.5380 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 CT2 222.500 1.5300 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT3 CA 230.000 1.4900 ! ALLOW ALI ARO
! toluene, adm jr. 3/7/92
CT3 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT3 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT3 CPB 230.000 1.4900 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT3 CPH1 229.630 1.5000 ! ALLOW ARO
! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
CT3 CS 190.000 1.5310 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
CT3 CT1 222.500 1.5380 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT2 222.500 1.5280 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT3 222.500 1.5300 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CY CA 350.000 1.3650 ! ALLOW ARO
!adm jr., 5/08/91, indole CCDB structure search
CY CPT 350.000 1.4400 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CY CT2 230.000 1.5100 ! ALLOW ARO
!JWK Kb from alkane freq.. b0 from TRP crystal
FE CM 258.000 1.9000 ! ALLOW HEM
! Heme (6-liganded): CO ligand (KK 05/13/91)
FE CPM 0.000 3.3814 ! ALLOW HEM
! Heme (6-liganded): for "ic para" only (KK 05/13/91)
H CD 330.000 1.1100 ! ALLOW PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
!HA C 330.000 1.1000 ! ALLOW ARO HEM
! Heme vinyl substituent (KK, from propene (JCS))
HA CA 340.000 1.0830 ! ALLOW ARO
! trp, adm jr., 10/02/89
HA CC 317.130 1.1000 ! ALLOW POL
! adm jr., 5/13/91, formamide geometry and vibrations
HA CP2 309.000 1.1110 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 309.000 1.1110 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CPM 367.600 1.0900 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
HA CS 300.000 1.1110 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CT1 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT2 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT3 322.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CY 330.000 1.0800 ! ALLOW ARO
! JWK 05/14/91 new r0 from indole
HE1 CE1 360.500 1.1000 !
! for propene, yin/adm jr., 12/95
HE2 CE2 365.000 1.1000 !
! for ethene, yin/adm jr., 12/95
HB CP1 330.000 1.0800 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CT1 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT2 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT3 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HP CA 340.000 1.0800 ! ALLOW ARO
! phe,tyr JES 8/25/89
HP CY 350.000 1.0800 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
HR1 CPH1 375.000 1.0830 ! ALLOW ARO
! his, adm jr., 6/27/90
HR1 CPH2 340.000 1.0900 ! ALLOW ARO
! his, adm jr., 6/28/29
HR2 CPH2 333.000 1.0700 ! ALLOW ARO
! his, adm jr., 6/27/90
HR3 CPH1 365.000 1.0830 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HT HT 0.000 1.5139 ! ALLOW WAT
! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM)
N C 260.000 1.3000 ! ALLOW PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 320.000 1.4340 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP3 320.000 1.4550 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC2 C 463.000 1.3650 ! ALLOW PEP POL ARO
! 403.0->463.0, 1.305->1.365 guanidinium (KK)
NC2 CT2 261.000 1.4900 ! ALLOW ALI POL
! arg, (DS)
NC2 CT3 261.000 1.4900 ! ALLOW ALI POL
! methylguanidinium, adm jr., 3/26/92
NC2 HC 455.000 1.0000 ! ALLOW POL
! 405.0->455.0 GUANIDINIUM (KK)
NH1 C 370.000 1.3450 ! ALLOW PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 320.000 1.4300 ! ALLOW ALI PEP POL ARO
! NMA Gas & Liquid Phase IR Spectra (LK)
NH1 CT2 320.000 1.4300 ! ALLOW ALI PEP POL ARO
! NMA Gas & Liquid Phase IR Spectra (LK)
NH1 CT3 320.000 1.4300 ! ALLOW ALI PEP POL ARO
! NMA Gas & Liquid Phase IR Spectra (LK)
NH1 H 440.000 0.9970 ! ALLOW PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 HC 405.000 0.9800 ! ALLOW PEP POL ARO
! (DS)
NH2 CC 430.000 1.3600 ! ALLOW PEP POL ARO
! adm jr. 4/10/91, acetamide
NH2 CT2 240.000 1.4550
! from NH2 CT3, neutral glycine, adm jr.
NH2 CT3 240.000 1.4550 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
NH2 H 480.000 1.0000 ! ALLOW POL
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 HC 460.000 1.0000 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
NH3 CT1 200.000 1.4800 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 CT2 200.000 1.4800 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 CT3 200.000 1.4800 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 HC 403.000 1.0400 ! ALLOW POL
! new stretch and bend; methylammonium (KK 03/10/92)
NP CP1 320.000 1.4850 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP3 320.000 1.5020 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP HC 460.000 1.0060 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NPH CPA 377.200 1.3757 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH FE 270.200 1.9580 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NR1 CPH1 400.000 1.3800 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR1 CPH2 400.000 1.3600 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR1 H 466.000 1.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 CPH1 400.000 1.3800 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 CPH2 400.000 1.3200 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 FE 65.000 2.2000 ! ALLOW HEM
! Heme (6-liganded): His ligand (KK 05/13/91)
NR3 CPH1 380.000 1.3700 ! ALLOW ARO
! his, adm jr., 6/28/90
NR3 CPH2 380.000 1.3200 ! ALLOW ARO
! his, adm jr., 6/27/90
NR3 H 453.000 1.0000 ! ALLOW ARO
! his, adm jr., 6/27/90
NY CA 270.000 1.3700 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
NY CPT 270.000 1.3750 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
NY H 465.000 0.9760 ! ALLOW ARO
! indole JWK 08/28/89
O C 620.000 1.2300 ! ALLOW PEP POL ARO
! Peptide geometry, condensed phase (LK)
O CC 650.000 1.2300 ! ALLOW PEP POL ARO
! adm jr. 4/10/91, acetamide
OB CC 750.000 1.2200 ! ALLOW PEP POL ARO
! adm jr., 10/17/90, acetic acid vibrations and geom.
OB CD 750.000 1.2200 ! ALLOW PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
OC CA 525.000 1.2600 ! ALLOW PEP POL ARO ION
! adm jr. 8/27/91, phenoxide
OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION
! adm jr. 7/23/91, acetic acid
OC CT2 450.000 1.3300 ! ALLOW ALC
! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
OC CT3 450.000 1.3300 ! ALLOW ALC
! methoxide 6-31+G* geom/freq, adm jr., 6/1/92
OH1 CA 334.300 1.4110 ! ALLOW ARO ALC
! MeOH, EMB 10/10/89,
OH1 CD 230.000 1.4000 ! ALLOW PEP POL ARO ALC
! adm jr. 5/02/91, acetic acid pure solvent
OH1 CT1 428.000 1.4200 ! ALLOW ALI ALC ARO
! methanol vib fit EMB 11/21/89
OH1 CT2 428.000 1.4200 ! ALLOW ALI ALC ARO
! methanol vib fit EMB 11/21/89
OH1 CT3 428.000 1.4200 ! ALLOW ALI ALC ARO
! methanol vib fit EMB 11/21/89
OH1 H 545.000 0.9600 ! ALLOW ALC ARO
! EMB 11/21/89 methanol vib fit
OM CM 1115.000 1.1280 ! ALLOW HEM
! Heme (6-liganded): CO ligand (KK 05/13/91)
OM FE 250.000 1.8000 ! ALLOW HEM
! Heme (6-liganded): O2 ligand (KK 05/13/91)
OM OM 600.000 1.2300 ! ALLOW HEM
! Heme (6-liganded): O2 ligand (KK 05/13/91)
OS CD 150.000 1.3340 ! ALLOW POL PEP
! adm jr. 5/02/91, acetic acid pure solvent
OS CT3 340.000 1.4300 ! ALLOW POL PEP
! adm jr., 4/05/91, for PRES CT1 from methylacetate
OT HT 450.000 0.9572 ! ALLOW WAT
! FROM TIPS3P GEOM
S CT2 198.000 1.8180 ! ALLOW ALI SUL ION
! fitted to C-S s 9/26/92 (FL)
S CT3 240.000 1.8160 ! ALLOW ALI SUL ION
! fitted to C-S s 9/26/92 (FL)
S HS 275.000 1.3250 ! ALLOW SUL ION
! methanethiol pure solvent, adm jr., 6/22/92
SM CT2 214.000 1.8160 ! ALLOW SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
SM CT3 214.000 1.8160 ! ALLOW SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
SM SM 173.000 2.0290 ! ALLOW SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
SS CS 205.000 1.8360 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
!lipid section
CTL3 CL 200.0 1.522 ! methyl acetate
CTL2 CL 200.0 1.522 ! methyl acetate
CTL1 CL 200.0 1.522 ! methyl acetate
OBL CL 750.0 1.220 ! methyl acetate
OCL CL 525.0 1.260 ! acetate, protein
OSL CL 150.0 1.334 ! methyl acetate
OHL CL 230.0 1.40 ! methyl acetate
HOL OHL 545.0 0.960 ! acetic acid
CTL1 HAL1 309.00 1.111 ! alkanes, 3/92
CTL2 HAL2 309.00 1.111 ! alkanes, 4/98
CTL3 HAL3 322.00 1.111 ! alkanes, 4/98
CTL3 OSL 340.0 1.43 ! phosphate
CTL2 OSL 340.0 1.43 ! phosphate
CTL1 OSL 340.0 1.43 ! phosphate
OSL PL 270.0 1.60 ! phosphate
O2L PL 580.0 1.48 ! phosphate
OHL PL 237.0 1.59 ! phosphate
NH3L HCL 410.0 1.04 ! ethanolamine
NH3L CTL2 261.0 1.51 ! ethanolamine
NTL CTL2 215.00 1.51 ! tetramethylammonium
NTL CTL5 215.00 1.51 ! tetramethylammonium
CTL5 HL 300.00 1.08 ! tetramethylammonium
CTL2 HL 300.00 1.08 ! tetramethylammonium
CTL1 CTL1 222.500 1.500 ! alkanes, 3/92
CTL1 CTL2 222.500 1.538 ! alkanes, 3/92
CTL1 CTL3 222.500 1.538 ! alkanes, 3/92
CTL2 CTL2 222.500 1.530 ! alkanes, 3/92
CTL2 CTL3 222.500 1.528 ! alkanes, 3/92
CTL3 CTL3 222.500 1.530 ! alkanes, 3/92
OHL CTL1 428.0 1.420 ! glycerol
OHL CTL2 428.0 1.420 ! glycerol
OHL CTL3 428.0 1.420 ! glycerol
SL O2L 540.0 1.448 ! methylsulfate
SL OSL 250.0 1.575 ! methylsulfate
!HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM)
!HT OT 450.0 0.9572 ! from TIPS3P geometry
CEL2 CEL2 510.000 1.330 ! ethene yin,adm jr., 12/95
HEL2 CEL2 365.000 1.100 ! propene; from ethene, yin,adm jr., 12/95
CEL1 CTL3 383.000 1.504 ! butene, yin,adm jr., 12/95
CEL1 CEL2 500.000 1.342 ! propene, yin,adm jr., 12/95
HEL1 CEL1 360.500 1.100 ! propene, yin,adm jr., 12/95
CEL1 CTL2 365.000 1.502 ! butene; from propene, yin,adm jr., 12/95
CEL1 CEL1 440.000 1.340 ! butene, yin,adm jr., 12/95
ANGLES
!
!V(angle) = Ktheta(Theta - Theta0)**2
!
!V(Urey-Bradley) = Kub(S - S0)**2
!
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley)
!S0: A
!
!atom types Ktheta Theta0 Kub S0
!
!Carbon Dioxide, JES
OST CST OST 3000.00 180.0000 ! CO2, JES
!Heme to Sulfate (PSUL) link
CS SS FE 50.0 100.6 !force constant a guess
!equilibrium angle optimized to reproduce
!CSD survey values
!107.5pm0.6 (mean, standard error)
!adm jr., 7/01
SS FE NPH 100.0 90.0 !force constant a guess
!adm jr., 7/01
!
CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO
! JES 8/25/89
CE1 CE1 CT2 48.00 123.50 !
! for 2-butene, yin/adm jr., 12/95
CE1 CE1 CT3 48.00 123.50 !
! for 2-butene, yin/adm jr., 12/95
CE1 CT2 CT3 32.00 112.20 !
! for 1-butene; from propene, yin/adm jr., 12/95
CE2 CE1 CT2 48.00 126.00 !
! for 1-butene; from propene, yin/adm jr., 12/95
CE2 CE1 CT3 47.00 125.20 !
! for propene, yin/adm jr., 12/95
CP1 N C 60.000 117.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 C 52.000 112.3000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 CC 52.000 112.3000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 CD 50.000 112.3000 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP2 CP1 70.000 108.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 CP2 CP2 70.000 108.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 N C 60.000 117.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 N CP1 100.000 114.2000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 NP CP1 100.000 111.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CPA CPB CE1 70.000 126.7400 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CPA CPM CPA 94.200 125.1200 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPA NPH CPA 139.300 103.9000 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB CE1 CE2 70.000 121.5000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CPB CPB CE1 70.000 126.7500 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CPB CPB CPA 30.800 106.5100 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPH2 NR1 CPH1 130.000 107.5000 ! ALLOW ARO
! his, adm jr., 6/27/90
CPH2 NR2 CPH1 130.000 104.0000 ! ALLOW ARO
! his, adm jr., 6/27/90
CPH2 NR3 CPH1 145.000 108.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
CPM CPA CPB 61.600 124.0700 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPT CA CA 60.000 118.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CPT CPT CA 60.000 122.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CPT CY CA 120.000 107.40 25.00 2.26100 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CPT NY CA 110.000 108.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CT1 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
CT1 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT1 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO
! PARALLH19 (JES)
CT1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
CT1 CT2 CPH1 58.350 113.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted
CT1 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT1 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
CT2 CA CA 45.800 122.3000 ! ALLOW ALI ARO
! PARALLH19 (JES)
CT2 CPB CPA 65.000 126.7400 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT2 CPB CPB 65.000 126.7500 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT2 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS
CT2 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
CT2 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
CT2 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 CT2 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! from CT2 CT1 C, for lactams, adm jr.
CT2 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
CT2 CT2 CPB 70.000 113.0000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT2 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT2 CT2 CT2 58.350 113.60 11.16 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 CT3 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT2 CY CA 45.800 129.4000 ! ALLOW ARO
!adm jr., 5/08/91, indole CCDB structure search
CT2 CY CPT 45.800 124.0000 ! ALLOW ARO
!adm jr., 5/08/91, indole CCDB structure search
CT2 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO
! 107.5->120.0 to make planar Arg (KK)
CT2 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
CT2 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP
! adm jr. 5/02/91, acetic acid pure solvent
CT3 CA CA 45.800 122.3000 ! ALLOW ALI ARO
! toluene, adm jr., 3/7/92
CT3 CPB CPA 65.000 126.7400 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT3 CPB CPB 65.000 126.7500 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT3 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS
CT3 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/09/92, for ALA cter
CT3 CT1 CT1 53.350 108.50 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT1 CT2 53.350 114.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT1 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO
! ethylbenzene, adm jr., 3/7/92
CT3 CT2 CPH1 58.350 113.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted
CT3 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT3 CT2 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT2 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO
! methylguanidinium, adm jr., 3/26/92
CT3 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
CT3 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP
! adm jr. 5/02/91, acetic acid pure solvent
CT3 S CT2 34.000 95.0000 ! ALLOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
CY CPT CA 160.000 130.6000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CY CPT CPT 110.000 107.4000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CY CT2 CT1 58.350 114.0000 ! ALLOW ARO
! from TRP crystal, JWK
CY CT2 CT3 58.350 114.0000 ! ALLOW ARO
! from TRP crystal, JWK
FE NPH CPA 96.150 128.0500 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
FE NR2 CPH1 30.000 133.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
FE NR2 CPH2 30.000 123.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
H NH1 C 34.000 123.0000 ! ALLOW PEP POL ARO
! NMA Vib Modes (LK)
H NH1 CT1 35.000 117.0000 ! ALLOW PEP POL ARO ALI
! NMA Vibrational Modes (LK)
H NH1 CT2 35.000 117.0000 ! ALLOW PEP POL ARO ALI
! NMA Vibrational Modes (LK)
H NH1 CT3 35.000 117.0000 ! ALLOW PEP POL ARO ALI
! NMA Vibrational Modes (LK)
H NH2 CC 50.000 120.0000 ! ALLOW POL PEP ARO
! his, adm jr. 8/13/90 acetamide geometry and vibrations
H NH2 H 23.000 120.0000 ! ALLOW POL
! adm jr. 8/13/90 acetamide geometry and vibrations
H NR1 CPH1 30.000 125.50 20.00 2.15000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NR1 CPH2 30.000 127.00 20.00 2.14000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NR3 CPH1 25.000 126.00 15.00 2.13000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NR3 CPH2 25.000 126.00 15.00 2.09000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NY CA 28.000 126.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
H NY CPT 28.000 126.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
H OH1 CA 65.000 108.0000 ! ALLOW ALC ARO
! JES 8/25/89 phenol
H OH1 CD 55.000 115.0000 ! ALLOW ALC ARO PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
H OH1 CT1 57.500 106.0000 ! ALLOW ALC ARO ALI
! methanol vib fit EMB 11/21/89
H OH1 CT2 57.500 106.0000 ! ALLOW ALC ARO ALI
! methanol vib fit EMB 11/21/89
H OH1 CT3 57.500 106.0000 ! ALLOW ALC ARO ALI
! methanol vib fit EMB 11/21/89
!HA C C 50.000 120.5000 ! ALLOW PEP POL ARO
! Heme vinyl substituent (KK from propene (JCS))
!HA C CPB 50.000 120.0000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
!HA C HA 50.000 118.0000 ! ALLOW PEP POL ARO
! Heme vinyl substituent (KK from propene (JCS))
HA CA CA 29.000 120.00 25.00 2.15250 ! ALLOW ARO
! trp, adm jr., 10/02/89
HA CA CPT 41.000 122.0000 ! ALLOW ARO
!adm jr., 5/08/91, indole CCDB structure search
HA CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HA CP2 CP1 33.430 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP2 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP2 CP3 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CPM CPA 12.700 117.4400 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
HA CPM FE 0.000 180.0000 ! ALLOW HEM
! Heme (6-liganded): for "ic para" only (KK 05/13/91)
HA CS CT3 34.600 110.10 22.53 2.17900 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CS HA 35.500 108.40 14.00 1.77500 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CT1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA CT1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA CT1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT1 HA 35.500 109.00 5.40 1.80200 ! TEST for test cpd
! based on HA CT2 HA
HA CT2 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA CT2 CA 49.300 107.5000 ! ALLOW ALI ARO
! PARALLH19 (JES)
HA CT2 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HA CT2 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA CT2 CE1 45.00 111.50 !
! for 1-butene; from propene, yin/adm jr., 12/95
HA CT2 CPB 50.000 109.5000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
HA CT2 CPH1 33.430 109.5000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
HA CT2 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
HA CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT2 CY 33.430 109.5000 ! ALLOW ARO
! ADM JR., 10/02/89, from CT2CT2HA (U-B OMITTED), FOR JOANNA
HA CT2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT3 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA CT3 CA 49.300 107.5000 ! ALLOW ALI ARO
! toluene, adm jr. 3/7/92
HA CT3 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HA CT3 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA CT3 CE1 42.00 111.50 !
! for 2-butene, yin/adm jr., 12/95
HA CT3 CPB 50.000 109.5000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
HA CT3 CPH1 33.430 109.5000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
HA CT3 CS 34.600 110.10 22.53 2.17900 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
HA CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CY CA 20.000 126.40 25.00 2.18600 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HA CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HE1 CE1 CE1 52.00 119.50 !
! for 2-butene, yin/adm jr., 12/95
HE1 CE1 CE2 42.00 118.00 !
! for propene, yin/adm jr., 12/95
HE1 CE1 CT2 40.00 116.00 !
! for 1-butene; from propene, yin/adm jr., 12/95
HE1 CE1 CT3 22.00 117.00 !
! for propene, yin/adm jr., 12/95
HE1 CE1 CPB 50.000 120.0000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
HE2 CE2 CE1 45.00 120.50 !
! for propene, yin/adm jr., 12/95
HE2 CE2 CE2 55.50 120.50 !
! for ethene, yin/adm jr., 12/95
HE2 CE2 HE2 19.00 119.00 !
! for propene, yin/adm jr., 12/95
HB CP1 C 50.000 112.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CP1 CC 50.000 112.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CP1 CD 50.000 112.0000 ! ALLOW PEP POL PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CP1 CP2 35.000 118.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CT1 C 50.000 109.5000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT1 CC 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HB CT1 CD 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
HB CT1 CT1 35.000 111.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT1 CT2 35.000 111.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT1 CT3 35.000 111.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT2 C 50.000 109.5000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT2 CC 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HB CT2 CD 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
HB CT2 HB 36.000 115.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT3 C 50.000 109.5000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HC NC2 C 49.000 120.0000 ! ALLOW POL PEP ARO
! 35.3->49.0 GUANIDINIUM (KK)
HC NC2 CT2 40.400 120.0000 ! ALLOW POL ALI
! 107.5->120.0 to make planar Arg (KK)
HC NC2 CT3 40.400 120.0000 ! ALLOW POL ALI
! methylguanidinium, adm jr., 3/26/92
HC NC2 HC 25.000 120.0000 ! ALLOW POL
! 40.0->25.0 GUANIDINIUM (KK)
HC NH2 CT2 50.000 111.0000 ! ALLOW POL
! from HC NH2 CT3, neutral glycine, adm jr.
HC NH2 CT3 50.000 111.0000 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
HC NH2 HC 39.000 106.5000 ! ALLOW POL
! 40.0->25.0 GUANIDINIUM (KK)
HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
! new stretch and bend; methylammonium (KK 03/10/92)
HC NH3 CT2 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
! new stretch and bend; methylammonium (KK 03/10/92)
HC NH3 CT3 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
! new stretch and bend; methylammonium (KK 03/10/92)
HC NH3 HC 44.000 109.5000 ! ALLOW POL
! new stretch and bend; methylammonium (KK 03/10/92)
HC NP CP1 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HC NP CP3 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HC NP HC 51.000 107.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HP CA CA 30.000 120.00 22.00 2.15250 ! ALLOW ARO
! JES 8/25/89 benzene
HP CA CPT 30.000 122.00 22.00 2.14600 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
HP CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HP CY CA 32.000 126.40 25.00 2.18600 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
HP CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HR1 CPH1 CPH1 22.000 130.00 15.00 2.21500 ! ALLOW ARO
! adm jr., 6/27/90, his
HR3 CPH1 CPH1 25.000 130.00 20.00 2.20000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HS S CT2 38.800 95.0000 ! ALLOW SUL ION ALI
! methanethiol pure solvent, adm jr., 6/22/92
HS S CT3 43.000 95.0000 ! ALLOW SUL ION ALI
! methanethiol pure solvent, adm jr., 6/22/92
HT OT HT 55.000 104.5200 ! ALLOW WAT
! TIP3P GEOMETRY, ADM JR.
N C CP1 20.000 112.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT1 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT2 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT3 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 C 50.000 108.2000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 CC 50.000 108.2000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 CD 50.000 108.2000 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 CP2 70.000 110.8000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 HB 48.000 112.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP3 CP2 70.000 110.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP3 HA 48.000 108.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC2 C NC2 52.000 120.00 90.00 2.36420 ! ALLOW POL PEP ARO
! changed from 60.0/120.3 for guanidinium (KK)
NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL
! arg, (DS)
NC2 CT2 HA 51.500 107.5000 ! ALLOW ALI POL
! arg, (DS)
NC2 CT3 HA 51.500 107.5000 ! ALLOW ALI POL
! methylguanidinium, adm jr., 3/26/92
NH1 C CP1 80.000 116.5000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH1 C CT1 80.000 116.5000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
NH1 C CT2 80.000 116.5000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
NH1 C CT3 80.000 116.5000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
NH1 CT1 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
NH1 CT1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 5/02/91, acetic acid pure solvent
NH1 CT1 CT1 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 HB 48.000 108.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT2 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT2 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 5/20/92, for asn,asp,gln,glu and cters
NH1 CT2 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 5/02/91, acetic acid pure solvent
NH1 CT2 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! from NH1 CT1 CT2, for lactams, adm jr.
NH1 CT2 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO
! from NH1 CT3 HA, for lactams, adm jr.
NH1 CT2 HB 48.000 108.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT3 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO
! NMA crystal (JCS)
NH2 CC CP1 80.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH2 CC CT1 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 CC CT3 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 CC HA 44.000 111.00 50.00 1.98000 ! ALLOW POL
! adm jr., 5/13/91, formamide geometry and vibrations
NH2 CT2 HA 38.000 109.50 50.00 2.14000
!from NH2 CT3 HA, neutral lysine
NH2 CT2 HB 38.000 109.50 50.00 2.14000
!from NH2 CT3 HA, neutral glycine, adm jr.
NH2 CT2 CD 52.000 108.0000
!from CT2 CT2 CD, neutral glycine, adm jr.
NH2 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL
!from NH3 CT2 CT2, neutral lysine
NH2 CT3 HA 38.000 109.50 50.00 2.14000 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
NH3 CT1 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI
! new aliphatics, adm jr., 2/3/92
NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
NH3 CT1 CT1 67.700 110.0000 ! ALLOW ALI POL
! new aliphatics, adm jr., 2/3/92
NH3 CT1 CT2 67.700 110.0000 ! ALLOW ALI POL
! new aliphatics, adm jr., 2/3/92
NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL
! new aliphatics, adm jr., 2/3/92
NH3 CT1 HB 51.500 107.5000 ! ALLOW ALI POL PEP
! new aliphatics, adm jr., 2/3/92
NH3 CT2 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI
! alanine (JCS)
NH3 CT2 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
NH3 CT2 CD 43.700 110.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 5/02/91, acetic acid pure solvent
NH3 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL
! alanine (JCS)
NH3 CT2 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 CT2 HB 51.500 107.5000 ! ALLOW ALI POL PEP
! for use on NTER -- from NH3 CT2HA (JCS) -- (LK)
NH3 CT3 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NP CP1 C 50.000 106.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP1 CC 50.000 106.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP1 CD 50.000 106.0000 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP1 CP2 70.000 108.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP1 HB 51.500 107.5000 ! ALLOW ALI POL PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP3 CP2 70.000 108.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP3 HA 51.500 109.1500 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NPH CPA CPB 122.000 111.5400 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH CPA CPM 88.000 124.3900 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH FE CM 50.000 90.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
NPH FE CPM 0.000 45.0000 ! ALLOW HEM
! Heme (6-liganded): for "ic para" only (KK 05/13/91)
NPH FE NPH 14.390 90.0000 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NR1 CPH1 CPH1 130.000 106.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR1 CPH1 CT2 45.800 124.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC FROM CA CT2CT
NR1 CPH1 CT3 45.800 124.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC FROM CA CT2CT
NR1 CPH1 HR3 25.000 124.00 20.00 2.14000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
NR1 CPH2 HR1 25.000 122.50 20.00 2.14000 ! ALLOW ARO
! his, adm jr., 6/27/90
NR2 CPH1 CPH1 130.000 110.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 CPH1 CT2 45.800 120.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC FROM CA CT2CT
NR2 CPH1 HR3 25.000 120.00 20.00 2.14000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
NR2 CPH2 HR1 25.000 125.00 20.00 2.12000 ! ALLOW ARO
! his, adm jr., 6/27/90
NR2 CPH2 NR1 130.000 112.5000 ! ALLOW ARO
! his, adm jr., 6/27/90
NR2 FE CM 50.000 180.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
NR2 FE NPH 50.000 90.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
NR3 CPH1 CPH1 145.000 108.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR3 CPH1 CT2 45.800 122.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC FROM CA CT2CT
NR3 CPH1 HR1 22.000 122.00 15.00 2.18000 ! ALLOW ARO
! his, adm jr., 6/27/90
NR3 CPH2 HR2 32.000 126.00 25.00 2.14000 ! ALLOW ARO