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par_all27_prot_na.inp
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*>>>>>> Combined CHARMM All-Hydrogen Parameter File for <<<<<<<<<
*>>>>>>> CHARMM22 Proteins and CHARMM27 Nucleic Acids <<<<<<<<<<
*from
*>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<
*>>>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<
*>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
*>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
*and
* \\\\ CHARMM27 All-Hydrogen Nucleic Acid Parameter File ////
* \\\\\\\\\\\\\\\\\\ Developmental ////////////////////////
* Alexander D. MacKerell Jr. and Nicolas Foloppe
* August 1999
* All comments to ADM jr. email: alex,mmiris.ab.umd.edu
* telephone: 410-706-7442
*
! references
!
!PROTEINS
!
!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.
!
!PHOSPHOTYROSINE
!
!Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D. and Lim, C.
!Structural Characterization of the Phosphotyrosine Binding Region of a
!High-Affinity aSH2 Domain-Phosphopeptide Complex by Molecular Dynamics
!Simulation and Chemical Shift Calculations. Journal of the American
!Chemical Society, 1996, 118: 11265-11277.
!
!IONS (see lipid and nucleic acid topology and parameter files for
!additional ions
!
!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)
!
!NUCLEIC ACIDS
!
!Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for
!Nucleic Acids: 2) Parameter Optimization Based on Small Molecule and
!Condensed Phase Macromolecular Target Data. Journal of Computational
!Chemistry, 2000, 21:86-104.
!
!and
!
!MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for
!Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA
!and RNA in Solution. Journal of Computational
!Chemistry, 2000, 21:105-120.
!
!NAD(P)+, NAD(P)H and PPI
!
!Pavelites, J.J., Bash, P.A., Gao, J. and MacKerell, Jr., A.D. A
!Molecular Mechanics Force Field for NAD+, NADH, and the Pyrophosphate
!Groups of Nucleotides, Journal of Computational Chemistry, 1997, 18:
!221-239.
!
!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
!
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 C 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
CA ON2b 340.0 1.38 !phenol phosphate, 6/94, adm jr.
ON2b P 270.0 1.61 !phenol phosphate, 6/94, adm jr.
!nucleic acid section
!
!NICH parameters to maintain back compatibility following
!atom type switch from HN3 to HN6
CN3C HN6 374.0 1.09 !nadh/ppi, jjp1/adm jr. 7/95
CN3 HN6 350.0 1.09 !nadh, adm jr., 8/98
!
CN1 CN3 302.0 1.409 !U, adm jr. 11/97
CN1 CN3T 302.0 1.403 !T, adm jr. 11/97
CN1A CN3 302.0 1.480 !nad/ppi, jjp1/adm jr. 7/95
CN1 CN5G 302.0 1.360 !G, adm jr. 11/97
CN1A NN1 560.0 1.360 !nad/ppi, jjp1/adm jr. 7/95
CN1 NN2 380.0 1.367 !C, adm jr. 11/97
CN1T NN2B 302.0 1.348 !U,T adm jr. 11/97
CN1 NN2G 340.0 1.396 !G, adm jr. 11/97
CN1 NN2U 340.0 1.389 !U,T adm jr. 11/97
CN1T NN2U 340.0 1.383 !U,T adm jr. 11/97
CN1 NN3 350.0 1.335 !C, adm jr. 11/97
CN1 ON1 660.0 1.234 !U,A,G par_a4 adm jr. 10/2/91
CN1A ON1 860.0 1.230 !nad/ppi, jjp1/adm jr. 7/95
CN1T ON1 860.0 1.230 !nad/ppi, jjp1/adm jr. 7/95
CN1 ON1C 620.0 1.245 !C, adm jr. 10/2/91
CN2 CN3 320.0 1.406 !C, adm jr. 11/97
CN2 CN3D 260.0 1.405 !5mc, adm jr. 9/9/93, from cn2 cn3
CN2 CN5 360.0 1.358 !A, adm jr. 11/97
CN2 NN1 360.0 1.366 !C,A,G JWK, adm jr. 10/2/91
CN2 NN2G 400.0 1.392 !G
CN2 NN3 450.0 1.343 !C
CN2 NN3A 400.0 1.342 !A, adm jr. 11/97
CN2 NN3G 320.0 1.326 !G, adm jr. 11/97
CN3 CN3 500.0 1.326 !C,U adm jr. 11/97
CN3 CN3T 560.0 1.320 !T, adm jr. 11/97
CN3A CN3 450.0 1.360 !nad/ppi, jjp1/adm jr. 7/95
CN3B CN3 420.0 1.350 !nad/ppi, jjp1/adm jr. 7/95
CN3C CN3 420.0 1.320 !nadh/ppi, jjp1/adm jr. 7/95
CN3D CN3 560.0 1.335 !5mc, adm jr. 9/9/93, from cn3 cn3
CN3 CN8 222.5 1.490 !nadh/ppi, jjp1/adm jr. 7/95
CN3D CN9 230.0 1.480 !5mc, adm jr. 9/9/93, from cn3 cn9
CN3T CN9 230.0 1.478 !T, adm jr. 11/97
CN3 HN3 350.0 1.09 !C,U, JWK
CN3T HN3 350.0 1.09 !T, JWK
CN3 HN3B 350.0 1.09 !nad/ppi, jjp1/adm jr. 7/95
CN3A HN3B 350.0 1.09 !nad/ppi, jjp1/adm jr. 7/95
CN3B HN3B 350.0 1.09 !nad/ppi, jjp1/adm jr. 7/95
CN3C HN3 374.0 1.09 !nadh/ppi, jjp1/adm jr. 7/95
CN3 NN2 302.0 1.343 !C, adm jr. 11/97
CN3 NN2B 320.0 1.343 !U,T adm jr. 11/97
CN3B NN2 420.0 1.315 !nad/ppi, jjp1/adm jr. 7/95
CN3C NN2 420.0 1.355 !nadh/ppi, jjp1/adm jr. 7/95
CN4 HN3 380.0 1.09 !G,A, JWK par_a7 9/30/91
CN4 NN2 320.0 1.374 !A, adm jr. 11/97
CN4 NN2B 300.0 1.378 !G, adm jr. 11/97
CN4 NN2G 350.0 1.365 !Inosine, adm jr. 2/94
CN4 NN3A 420.0 1.322 !A, adm jr. 11/97
CN4 NN3I 450.0 1.295 !Inosine, adm jr. 2/94
CN4 NN4 400.0 1.305 !G,A, adm jr. 11/97
CN5 CN5 310.0 1.361 !A, adm jr. 11/97
CN5 CN5G 320.0 1.350 !G, adm jr. 11/97
CN5 NN2 300.0 1.375 !A, adm jr. 11/97
CN5 NN2B 302.0 1.375 !G, adm jr. 11/97
CN5 NN3A 350.0 1.312 !A, JWK par_a8 9/30/91
CN5 NN3G 350.0 1.315 !G, adm jr. 11/97
CN5 NN3I 350.0 1.332 !Inosine, adm jr. 9/98
CN5 NN4 310.0 1.355 !A, adm jr. 11/97
CN5G NN4 310.0 1.365 !G, adm jr. 11/97
CN8 CN8 222.50 1.528 !Alkanes, sacred
CN8 CN9 222.50 1.528 !Alkanes, sacred
CN8 NN2 400.0 1.460 !9-E-GUA, ADM JR.
CN8 ON5 428.0 1.42 !RIBOSE, MeOH
CN9 HN9 322.0 1.111 !alkanes
CN9 ON2 340.0 1.43 !DMP, ADM Jr.
HN1 NN1 488.0 1.00 !A,C,G, JWK, adm jr. 7/24/91
HN2 NN2 474.0 1.01 !C,U, JWK
HN2 NN2B 474.0 1.01 !G, adm jr. 11/97
HN2 NN2G 471.0 1.01 !G, JWK, par_a12 9/30/91
HN2 NN2U 474.0 1.01 !U, JWK, adm jr. 7/24/91
HN4 ON4 545.0 0.960 !MP_1, ADM Jr.
!HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM)
!HT OT 450.0 0.9572 ! from TIPS3P geometry
ON2 P 270.0 1.60 !DMP, ADM Jr.
ON3 P 580.0 1.48 !DMP, ADM Jr.
ON4 P 237.0 1.58 !MP_1, ADM Jr.
ON2 P2 300.0 1.68 !nad/ppi, jjp1/adm jr. 7/95
ON3 P2 480.0 1.53 !nad/ppi, jjp1/adm jr. 7/95
NN5 HN1 460.0 1.01 !sugar model, adm jr.
!@@@@@@@@@ Begining of endocyclic bonds for deoxy-ribose @@@@@@@@@
CN7B ON6 260.0 1.420 ! From exp
CN7B CN8 200.0 1.518 ! From exp
CN7 ON6 240.0 1.446 ! Fom exp.
CN7 CN8 222.5 1.516 ! From exp.
CN7 CN7 222.5 1.529 ! From exp
CN7 HN7 309.0 1.111 !Alkanes, sacred
CN8 HN8 309.0 1.111 !Alkanes, sacred
CN7B HN7 309.0 1.111 ! From CN8 HN7 (NF)
!@@@@@@@@@ End of endocyclic bonds for deoxy-ribose @@@@@@@@@
!@@@@@@@@@ Begining of endocyclic bonds for ribose @@@@@@@@@
CN7B ON6B 260.0 1.420 ! From CN7B ON6
CN7 ON6B 240.0 1.480 ! From CN7 ON6
CN7B CN7B 200.0 1.450 !
CN7 CN7B 222.5 1.460 ! Specific to RNA
!@@@@@@@@@ End of endocyclic bonds for ribose @@@@@@@@@
!@@@@@@@@@ Begining of endocyclic bonds for arabinose @@@@@@@@@
! Transfered from DNA
CN7B CN7C 200.0 1.518 ! For arabinose, from CN7B CN8
CN7 CN7C 222.5 1.516 ! For arabinose, from CN7 CN8
CN7C HN7 309.0 1.111 ! From CN8 HN7
!@@@@@@@@@ End of endocyclic bonds for arabinose @@@@@@@@@
!@@@@@@@@@ Begining of exocyclic bonds for deoxy-ribose @@@@@@@@@
CN7 CN8B 222.5 1.512 ! From exp.
CN8B ON2 320.0 1.44 ! From exp
!CN8B ON5 250.0 1.44 ! From CN8B ON2
CN8B ON5 428.0 1.42 !From CN8 ON2, adm jr., 8/30/98
CN7 ON2 310.0 1.433 ! From exp
CN7B ON2 310.0 1.433 ! From exp, for NADPH etc.
!CN7 ON5 250.0 1.420 ! ALLOW ALI ALC ARO
CN7 ON5 428.0 1.42 !From CN8 ON2, adm jr., 8/30/98
! C1'-N9 (purines)/C1'-N1 (pyrimidines)
CN9 NN2 400.0 1.456 !9-M-A/C, adm jr.
CN8 NN2B 400.0 1.458 !9-M-G/T/U, adm jr.
CN9 NN2B 400.0 1.458 !9-M-G/T/U, adm jr.
CN7B NN2 220.0 1.456 !A/C
CN7B NN2B 220.0 1.458 !G/T/U
! C5'-H in model compounds and DNA
CN8B HN8 309.0 1.111 !Alkanes, sacred
ON5 HN5 545.0 0.960 !RIBOSE, MeOH
!@@@@@@@@@ End of exocyclic bonds for deoxy-ribose @@@@@@@@@
!@@@@@@@@@ Begining of exocyclic bonds for ribose @@@@@@@@@
!CN7B ON5 250.0 1.400 ! From CN7 ON5
CN7B ON5 428.0 1.400 ! check adm jr.,
!FC should be 428.000 based on Meoh
!@@@@@@@@@ End of exocyclic bonds for ribose @@@@@@@@@
!@@@@@@@@@ Begining of exocyclic bonds for arabinose @@@@@@@@@
!CN7C ON5 250.0 1.400 ! From CN7 ON5
CN7C ON5 428.0 1.400 ! check adm jr.,
!FC should be 428.000 based on Meoh
!@@@@@@@@@ End of exocyclic bonds for arabinose @@@@@@@@@
!@@@@@@@@@ Begining of bonds for nucleotide analogue @@@@@@@@@
CN8 ON2 340.0 1.44 !
!@@@@@@@@@ End of bonds for nucleotide analogue @@@@@@@@@
! C1'-ND1 in imidazole model compound
CN7B NR1 220.000 1.4620 ! From crystal nucleosides A/G (NF)
!NR1 CPH1 400.000 1.3800 ! From imidazole (NF)
!NR1 CPH2 400.000 1.3600 ! From imidazole (NF)
!NR2 CPH1 400.000 1.3800 ! From imidazole (NF)
!NR2 CPH2 400.000 1.3200 ! From imidazole (NF)
!CPH1 CPH1 410.000 1.3600 ! From imidazole (NF)
!HR1 CPH2 340.000 1.0900 ! From imidazole (NF)
!HR3 CPH1 365.000 1.0830 ! From imidazole (NF)
CA OJ2 455.0 1.23
CA OJ1 350.0 1.319
SJ O 660.0 1.425 ! **added by jbardhan, 7/25/04
SJ OJ2 528.0 1.50
SJ OE 260.0 1.57
SJ OJ1 237.0 1.54
SJ OT 260.0 1.585
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
!
CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO
! JES 8/25/89
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 C 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 C C 70.000 121.5000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CPB CPB C 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
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