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top_all36_prot.prm
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top_all36_prot.prm
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*>>>> CHARMM36 All-Hydrogen Parameter File for Proteins <<<<<<<<<<
*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<<
*>>>>>>>>>>>>>>>>>>>>>>>>>> Feb. 2012 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
* All comments to the CHARMM web site: www.charmm.org
* parameter set discussion forum
*
!references
!
!Robert B. Best, R.B., Xiao Zhu, X., Shim, J., Lopes, P.
!Mittal, J., Feig, M. and MacKerell, A.D., Jr. Optimization of the
!additive CHARMM all-atom protein force field targeting improved
!sampling of the backbone phi, psi and sidechain chi1 and chi2
!dihedral angles. In preparation
!
!MacKerell, A.D., Jr., Feig, M. and Brooks, III, C.L. "Improved
!treatment of the protein backbone in empirical force fields," Journal
!of the American Chemical Society, 126: 698-699, 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.
ATOMS
MASS -1 H 1.00800 ! polar H
MASS -1 HC 1.00800 ! N-ter H
MASS -1 HA 1.00800 ! nonpolar H
MASS -1 HP 1.00800 ! aromatic H
MASS -1 HB1 1.00800 ! backbone H
MASS -1 HB2 1.00800 ! aliphatic backbone H, to CT2
MASS -1 HR1 1.00800 ! his he1, (+) his HG,HD2
MASS -1 HR2 1.00800 ! (+) his HE1
MASS -1 HR3 1.00800 ! neutral his HG, HD2
MASS -1 HS 1.00800 ! thiol hydrogen
MASS -1 HE1 1.00800 ! for alkene; RHC=CR
MASS -1 HE2 1.00800 ! for alkene; H2C=CR
MASS -1 HA1 1.00800 ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS -1 HA2 1.00800 ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS -1 HA3 1.00800 ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS -1 C 12.01100 ! carbonyl C, peptide backbone
MASS -1 CA 12.01100 ! aromatic C
MASS -1 CT 12.01100 ! aliphatic sp3 C, new LJ params, no hydrogens, see retinol stream file for parameters
MASS -1 CT1 12.01100 ! aliphatic sp3 C for CH
MASS -1 CT2 12.01100 ! aliphatic sp3 C for CH2
MASS -1 CT2A 12.01100 ! from CT2 (GLU, HSP chi1/chi2 fitting) 05282010, zhu
MASS -1 CT3 12.01100 ! aliphatic sp3 C for CH3
MASS -1 CPH1 12.01100 ! his CG and CD2 carbons
MASS -1 CPH2 12.01100 ! his CE1 carbon
MASS -1 CPT 12.01100 ! trp C between rings
MASS -1 CY 12.01100 ! TRP C in pyrrole ring
MASS -1 CP1 12.01100 ! tetrahedral C (proline CA)
MASS -1 CP2 12.01100 ! tetrahedral C (proline CB/CG)
MASS -1 CP3 12.01100 ! tetrahedral C (proline CD)
MASS -1 CC 12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2
MASS -1 CD 12.01100 ! carbonyl C, pres aspp,glup,ct1
MASS -1 CS 12.01100 ! thiolate carbon
MASS -1 CE1 12.01100 ! for alkene; RHC=CR
MASS -1 CE2 12.01100 ! for alkene; H2C=CR
MASS -1 CAI 12.01100 ! aromatic C next to CPT in trp
MASS -1 N 14.00700 ! proline N
MASS -1 NR1 14.00700 ! neutral his protonated ring nitrogen
MASS -1 NR2 14.00700 ! neutral his unprotonated ring nitrogen
MASS -1 NR3 14.00700 ! charged his ring nitrogen
MASS -1 NH1 14.00700 ! peptide nitrogen
MASS -1 NH2 14.00700 ! amide nitrogen
MASS -1 NH3 14.00700 ! ammonium nitrogen
MASS -1 NC2 14.00700 ! guanidinium nitrogen
MASS -1 NY 14.00700 ! TRP N in pyrrole ring
MASS -1 NP 14.00700 ! Proline ring NH2+ (N-terminal)
MASS -1 O 15.99900 ! carbonyl oxygen
MASS -1 OB 15.99900 ! carbonyl oxygen in acetic acid
MASS -1 OC 15.99900 ! carboxylate oxygen
MASS -1 OH1 15.99900 ! hydroxyl oxygen
MASS -1 OS 15.99940 ! ester oxygen
MASS -1 S 32.06000 ! sulphur
MASS -1 SM 32.06000 ! sulfur C-S-S-C type
MASS -1 SS 32.06000 ! thiolate sulfur
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
NH2 CT1 240.000 1.4550 ! From LSN NH2-CT2
!
!Indole/Tryptophan
CA CAI 305.000 1.3750 ! from CA CA
CAI CAI 305.000 1.3750 ! atm, methylindole, fit CCDSS
CPT CA 300.000 1.3600 ! atm, methylindole, fit CCDSS
CPT CAI 300.000 1.3600 ! atm, methylindole, fit CCDSS
CPT CPT 360.000 1.3850 ! atm, methylindole, fit CCDSS
CY CA 350.000 1.3650 ! trj, adm jr., 5/08/91, indole CCDB structure search
CY CAI 350.000 1.3650 ! from CY CA
CY CPT 350.000 1.4300 ! atm, methylindole, fit CDS data
CY CT3 375.000 1.4920 ! atm, methylindole, fit CDS data
CY CT2 375.000 1.4920 ! atm, methylindole, fit CDS data
HP CAI 340.000 1.0800 ! from HP CA
HP CY 350.000 1.0800 ! trp, adm jr., 12/30/91
NY CA 270.000 1.3700 ! trp, adm jr., 12/30/91
NY CPT 270.000 1.3700 ! atm, methylindole, from CCDS 1/17/04
NY H 537.500 0.9760 ! atm, methylindole, 1/17/04
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
CPH1 CPH1 410.000 1.3600 ! ALLOW ARO
! histidine, adm jr., 6/27/90
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 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 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
H CD 330.000 1.1100 ! ALLOW PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA1 CC 317.130 1.1000 ! ALLOW POL
! adm jr., 5/13/91, formamide geometry and vibrations
HA2 CP2 309.000 1.1110 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA2 CP3 309.000 1.1110 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA2 CS 300.000 1.1110 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA3 CS 300.000 1.1110 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA1 CT1 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA2 CT2 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA3 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
HB1 CP1 330.000 1.0800 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB1 CT1 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB2 CT2 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
!HB3 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
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
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 450.000 1.3650 ! ALLOW PEP POL ARO
! mp2/6-311g** mgua vib. data, adm jr., 1/04
NC2 CT2 390.000 1.4900 ! ALLOW ALI POL
! mp2/6-311g** mgua vib. data, adm jr., 1/04
NC2 CT3 390.000 1.4900 ! ALLOW ALI POL
! mp2/6-311g** mgua vib. data, adm jr., 1/04
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
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
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
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
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
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 surface in DMDS 5/15/92 (FL)
SM CT3 214.000 1.8160 ! ALLOW SUL ION
! improved CSSC surface in DMDS 5/15/92 (FL)
SM SM 173.000 2.0290 ! ALLOW SUL ION
! improved CSSC surface 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
HR1 CD 330.000 1.1100 ! acetaldehyde, benzaldehyde, 3ALP
O CD 720.000 1.2050 ! acetaldehyde, benzaldehyde, 3ALP. from stream/toppar_all27_na_bkb_modifications.str
CT2A CT1 222.500 1.5380 ! from CT2 CT1, Zhu
CT2 CT2A 222.500 1.5300 ! from CT2 CT2, Zhu
CT2A HA2 309.000 1.1110 ! from HA2 CT2, Zhu
CT2A CPH1 229.630 1.5000 ! from CT2 CPH1, Zhu
!ASP, CT2->CT2A
CT2A CC 200.000 1.5220 ! from CT2 CC, jshim
! RESI CYSM and PRES CYSD
CT1 CS 190.000 1.5380 ! from CT3 CS but lengthened; compare CT3 CT2 with CT2 CT1; kevo
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
!
H NH2 CT1 50.000 111.00 ! From LSN HC-NH2-CT2
H NH2 CT2 50.000 111.00 ! From LSN HC-NH2-CT2, Neutral Gly Nterminus
NH2 CT1 CT1 67.700 110.00 ! From LSN NH2-CT2-CT2
NH2 CT1 CT2 67.700 110.00 ! From LSN NH2-CT2-CT2
NH2 CT1 CT2A 67.700 110.00 ! From LSN NH2-CT2-CT2
NH2 CT1 CT3 67.700 110.00 ! From LSN NH2-CT2-CT2
CT1 CD OH1 55.000 110.50 ! From ASPP CT2-CD-OH1
CT3 CT1 CD 52.000 108.00 ! Ala cter
NH2 CT1 HB1 38.000 109.50 50.00 2.1400 ! From LSN NH2-CT2-HA
NH2 CT1 C 50.000 107.00 ! From ALA Dipep. NH1-CT2-C
NH2 CT1 CD 50.000 107.00 ! From ALA Dipep. NH1-CT2-C
NH2 CT2 C 50.000 107.00 ! From ALA Dipep. NH1-CT2-C, Neutral Gly Nterminus
!NH2 CT2 CD 50.000 107.00 ! From ALA Dipep. NH1-CT2-C, Neutral Gly Nterminus, repeat, see below
HB2 CT1 HB2 36.000 115.00 ! from HB2 CT2 HB2
HB2 CT1 CD 50.000 109.50 ! from HB2 CT2 CD
NH1 CT1 HB2 48.000 108.00 ! from NH1 CT2 HB2
!
!Indole/Tryptophan
CAI CAI CA 40.000 120.00 35.00 2.41620 ! from CA CA CA
CAI CA CA 40.000 120.00 35.00 2.41620 ! from CA CA CA
CPT CA CA 50.000 113.20 ! atm, methylindole, 1/17/04
CPT CPT CA 50.000 110.00 ! atm, methylindole, 1/17/04
CPT CAI CA 50.000 113.20 ! atm, methylindole, 1/17/04
CPT CPT CAI 50.000 110.00 ! atm, methylindole, 1/17/04
CPT CY CA 85.000 106.40 25.00 2.26100 ! atm, methylindole, 1/17/04
CPT NY CA 85.000 112.00 ! atm, methylindole, 1/17/04
CT2 CY CA 30.000 127.00 ! atm, methylindole, CT3 CY CA
CT2 CY CPT 30.000 126.70 ! atm, methylindole, 1/17/04
CT3 CY CA 30.000 127.00 ! atm, methylindole, CT3 CY CA
CT3 CY CPT 30.000 126.70 ! atm, methylindole, 1/17/04
CY CPT CA 130.000 133.50 ! atm, methylindole, 1/17/04
CY CPT CAI 130.000 133.50 ! atm, methylindole, 1/17/04
CY CPT CPT 85.000 108.00 ! atm, methylindole, 1/17/04
CY CT2 CT1 58.350 114.00 ! from TRP crystal, JWK
CY CT2 CT3 58.350 114.00 ! from TRP crystal, JWK
H NY CA 28.000 126.00 ! trp, adm jr., 12/30/91
H NY CAI 28.000 126.00 ! trp, adm jr., 12/30/91
H NY CPT 28.000 126.00 ! trp, adm jr., 12/30/91
HA2 CT2 CY 55.000 109.50 ! atm, methylindole, 1/17/04
HA3 CT3 CY 55.000 109.50 ! atm, methylindole, 1/17/04
HP CA CAI 30.000 120.00 22.00 2.15250 ! from HP CA CA
HP CAI CA 30.000 120.00 22.00 2.15250 ! from HP CA CA
HP CA CPT 30.000 122.00 22.00 2.14600 ! trp, adm jr., 12/30/91
HP CAI CPT 30.000 122.00 22.00 2.14600 ! from HP CA CPT
HP CA CY 32.000 125.00 25.00 2.17300 ! JWK 05/14/91 new theta0 and r0UB from indole
HP CY CA 32.000 126.40 25.00 2.18600 ! trp, adm jr., 12/30/91
HP CY CPT 32.000 126.40 25.00 2.25500 ! JWK 05/14/91 new theta0 and r0UB from indole
NY CA CY 85.000 110.50 25.00 2.24000 ! trp, adm jr., 12/30/91
NY CA HP 32.000 125.00 25.00 2.17700 ! JWK 05/14/91 new theta0 and r0UB from indole
NY CPT CA 130.000 129.50 ! atm, methylindole, 1/17/04
NY CPT CAI 130.000 129.50 ! atm, methylindole, 1/17/04
NY CPT CPT 95.000 107.40 ! atm, methylindole, 1/17/04
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
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
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 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 6/27/2012, for Thr with CT1 patch
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 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
CT2A 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
CT3 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
CT2A CT2 CD 52.000 108.0000 ! for GLUP, ZHU
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 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 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)
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 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
HA2 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
HA2 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
HA2 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
HA2 CP2 HA2 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA2 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
HA2 CP3 HA2 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA2 CS CT3 34.600 110.10 22.53 2.17900 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA2 CS HA2 35.500 108.40 14.00 1.77500 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA3 CS HA3 35.500 108.40 14.00 1.77500 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA1 CT1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA1 CT1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA1 CT1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA1 CT1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA1 CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA1 CT1 HA1 35.500 109.00 5.40 1.80200 ! TEST for test cpd
! based on HA CT2 HA
HA2 CT2 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA2 CT2 CA 49.300 107.5000 ! ALLOW ALI ARO
! PARALLH19 (JES)
HA2 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
HA2 CT2 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA2 CT2 CE1 45.00 111.50 !
! for 1-butene; from propene, yin/adm jr., 12/95
HA2 CT2 CPH1 33.430 109.5000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
HA2 CT2 CT1 26.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
HA2 CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA2 CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA2 CT2 HA2 35.500 109.00 5.40 1.80200 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA3 CT3 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA3 CT3 CA 49.300 107.5000 ! ALLOW ALI ARO
! toluene, adm jr. 3/7/92
HA3 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
HA3 CT3 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA3 CT3 CE1 42.00 111.50 !
! for 2-butene, yin/adm jr., 12/95
HA3 CT3 CPH1 33.430 109.5000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
HA3 CT3 CS 34.600 110.10 22.53 2.17900 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA3 CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
HA3 CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA3 CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA3 CT3 HA3 35.500 108.40 5.40 1.80200 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
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
HB1 CP1 C 50.000 112.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB1 CP1 CC 50.000 112.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB1 CP1 CD 50.000 112.0000 ! ALLOW PEP POL PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB1 CP1 CP2 35.000 118.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB1 CT1 C 50.000 109.5000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB1 CT1 CC 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HB1 CT1 CD 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
HB1 CT1 CT1 35.000 111.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB1 CT1 CT2 35.000 111.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB1 CT1 CT3 35.000 111.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB2 CT2 C 50.000 109.5000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB2 CT2 CC 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HB2 CT2 CD 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
HB2 CT2 HB2 36.000 115.0000 ! 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
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
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 HB1 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 HA2 48.000 108.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC2 C NC2 40.000 120.00 70.00 2.31
! mp2/6-311g** mgua vib data, adm jr., 1/04
! N-N distances: 2.29001, 2.31146, 2.33240
NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL
! arg, (DS)
NC2 CT2 HA2 56.500 107.5000 ! ALLOW ALI POL
! mp2/6-311g** mgua vib data, adm jr., 1/04
NC2 CT3 HA3 56.5000 107.5000 ! ALLOW ALI POL
! mp2/6-311g** mgua vib data, adm jr., 1/04
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 HB1 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 HA2 51.500 109.5000 ! ALLOW ALI PEP POL ARO
! from NH1 CT3 HA, for lactams, adm jr.
NH1 CT2 HB2 48.000 108.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT3 HA3 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 HA1 44.000 111.00 50.00 1.98000 ! ALLOW POL
! adm jr., 5/13/91, formamide geometry and vibrations
NH2 CT2 HB2 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 CT2 HA2 38.000 109.50 50.00 2.14000
!from NH2 CT3 HA, neutral lysine
NH2 CT3 HA3 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 HB1 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
! methylammonium
NH3 CT2 CT3 67.700 110.0000 ! ALLOW ALI POL
! ethylammonium
NH3 CT2 HA2 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 CT2 HB2 51.500 107.5000 ! ALLOW ALI POL PEP
! for use on NTER -- from NH3 CT2HA (JCS) -- (LK)
NH3 CT3 HA3 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 HB1 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 HA2 51.500 109.1500 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
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
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
! his, adm jr., 6/27/90
NR3 CPH2 NR3 145.000 108.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
O C CP1 80.000 118.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O C CT1 80.000 121.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
O C CT2 80.000 121.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
O C CT3 80.000 121.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
O C H 50.000 121.7000 ! ALLOW PEP POL ARO
! acetaldehyde (JCS)
O C N 80.000 122.5000 ! ALLOW PRO PEP POL ARO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O C NH1 80.000 122.5000 ! ALLOW PEP POL ARO
! NMA Vib Modes (LK)
O CC CP1 80.000 118.0000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O CC CT1 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/10/91, acetamide update
O CC CT2 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/10/91, acetamide update
O CC CT3 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/10/91, acetamide update
O CC HA1 44.000 122.0000 ! ALLOW POL
! adm jr., 5/13/91, formamide geometry and vibrations
O CC NH2 75.000 122.50 50.00 2.37000 ! ALLOW POL PEP ARO
! adm jr. 4/10/91, acetamide update
OB CD CP1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
OB CD CT1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
OB CD CT2 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
OB CD CT3 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
OC CA CA 40.000 120.0000 ! ALLOW POL ARO
! adm jr. 8/27/91, phenoxide
OC CC CP1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION
! adm jr. 7/23/91, correction, ACETATE (KK)
OC CC CT2 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION
! adm jr. 7/23/91, correction, ACETATE (KK)
OC CC CT3 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION
! adm jr. 7/23/91, correction, ACETATE (KK)
OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO
! adm jr. 7/23/91, correction, ACETATE (KK)
OC CT2 CT3 65.000 122.0000 ! ALLOW ALC
! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
OC CT2 HA2 65.000 118.3000 ! ALLOW ALC
! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
OC CT3 HA3 65.000 118.3000 ! ALLOW ALC
! methoxide 6-31+G* geom/freq, adm jr., 6/1/92
OH1 CA CA 45.200 120.0000 ! ALLOW ARO ALC
! PARALLH19 WITH [122.3] (JES)
OH1 CD CT2 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC
! adm jr, 10/17/90, acetic acid vibrations
OH1 CD CT3 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC
! adm jr, 10/17/90, acetic acid vibrations
OH1 CD OB 50.000 123.00 210.00 2.26200 ! ALLOW PEP POL ARO ALC
! adm jr, 10/17/90, acetic acid vibrations
OH1 CT1 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT1 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT1 HA1 45.900 108.8900 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT2 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT2 CT2 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT2 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT2 HA2 45.900 108.8900 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT3 HA3 45.900 108.8900 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OS CD CP1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
OS CD CT1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP
! adm jr., 4/05/91, for PRES CT1 from methylacetate
OS CD CT2 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP
! adm jr., 4/05/91, for PRES CT1 from methylacetate
OS CD CT3 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP
! adm jr., 4/05/91, for PRES CT1 from methylacetate
OS CD OB 90.000 125.90 160.00 2.25760 ! ALLOW PEP POL
! adm jr. 3/19/92, from lipid methyl acetate
OS CT2 HA2 60.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for PRES CT1 from methyl acetate
OS CT3 HA3 60.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for PRES CT1 from methyl acetate
S CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION
! as in expt.MeEtS & DALC crystal, 5/15/92
S CT2 CT2 58.000 114.5000 ! ALLOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
S CT2 CT3 58.000 114.5000 ! ALLOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
S CT2 HA2 46.100 111.3000 ! ALLOW ALI SUL ION
! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90
S CT3 HA3 46.100 111.3000 ! ALLOW ALI SUL ION
! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90
SM CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION
! as in expt.MeEtS & DALC crystal, 5/15/92
SM CT2 CT3 58.000 112.5000 ! ALLOW ALI SUL ION
! diethyldisulfide, as in expt.MeEtS & DALC crystal, 5/15/92
SM CT2 HA2 38.000 111.0000 ! ALLOW ALI SUL ION
! new S-S atom type 8/24/90
SM CT3 HA3 38.000 111.0000 ! ALLOW ALI SUL ION
! new S-S atom type 8/24/90
SM SM CT2 72.500 103.3000 ! ALLOW ALI SUL ION
! expt. dimethyldisulfide, 3/26/92 (FL)
SM SM CT3 72.500 103.3000 ! ALLOW ALI SUL ION
! expt. dimethyldisulfide, 3/26/92 (FL)
SS CS CT3 55.000 118.0000 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
SS CS HA2 40.000 112.3000 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
SS CS HA3 40.000 112.3000 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
O CD HR1 75.000 121.0000 ! acetaldehyde, benzaldehyde, 3ALP, retinal
!For GLU/HSP, Zhu
NH1 CT1 CT2A 70.000 113.5000 ! from NH1 CT1 CT2
HB1 CT1 CT2A 35.000 111.0000 ! from HB1 CT1 CT2
CT2A CT1 C 52.000 108.0000 ! from CT2 CT1 C
CT1 CT2A HA2 26.500 110.1000 22.53 2.17900 ! from HA2 CT2 CT1
CT1 CT2A CT2 58.350 113.5000 11.16 2.56100 ! from CT2 CT2 CT1
HA2 CT2A HA2 35.500 109.0000 5.40 1.80200 ! from HA2 CT2 HA2
HA2 CT2A CT2 26.500 110.1000 22.53 2.17900 ! from HA2 CT2 CT2
CT2A CT2 HA2 26.500 110.1000 22.53 2.17900 ! from HA2 CT2 CT2