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Commit cc97a0ba authored by Jason Swails's avatar Jason Swails
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Add the parameter/RTF files back for the examples. Put a note in 

simulateCharmm.py to use the latest force fields. This is what CHARMM does for
their own tutorials, so this is fine.
parent 46c5f78f
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examples/charmm22.par 0 → 100644
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*>>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<
*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
*>>>>>>>>>>>>>>>>>>>>>> December, 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.
!
!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)
!
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
NH2 CT1 240.00 1.455 ! From LSN NH2-CT2
!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
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
NH2 CT1 CT2 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 HB 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
!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
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
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 CT3 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
! his, adm jr., 6/27/90
NR3 CPH2 NR3 145.000 108.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
NY CA CY 120.000 110.00 25.00 2.24000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
NY CA HA 32.000 125.00 25.00 2.17700 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
NY CA HP 32.000 125.00 25.00 2.17700 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
NY CPT CA 160.000 130.6000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
NY CPT CPT 110.000 107.4000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
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 HA 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 HA 65.000 118.3000 ! ALLOW ALC
! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
OC CT3 HA 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 HA 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 HA 45.900 108.8900 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT3 HA 45.900 108.8900 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OM CM FE 35.000 180.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
OM FE NPH 5.000 90.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
OM OM FE 0.000 180.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
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 HA 60.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for PRES CT1 from methyl acetate
OS CT3 HA 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 HA 46.100 111.3000 ! ALLOW ALI SUL ION
! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90
S CT3 HA 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 CT2 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
! as in expt.MeEtS & DALC crystal, 5/15/92
SM CT2 HA 38.000 111.0000 ! ALLOW ALI SUL ION
! new S-S atom type 8/24/90
SM CT3 HA 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 HA 40.000 112.3000 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types Kchi n delta
!
!Neutral N terminus
NH2 CT1 C O 0.0000 1 0.00
NH2 CT1 C NH1 0.0000 1 0.00
H NH2 CT1 CT1 0.0000 1 0.00
H NH2 CT1 C 0.000 1 0.00
H NH2 CT1 HB 0.110 3 0.00 ! From LSN HC-NH2-CT2-HA
H NH2 CT1 CT2 0.110 3 0.00 ! From LSN HC-NH2-CT2-CT2
H NH2 CT1 CT3 0.110 3 0.00 ! From LSN HC-NH2-CT2-CT2
!Heme to Sulfate (PSUL) link
X FE SS X 0.0000 4 0.00 ! guess
!adm jr., 7/01
X CS SS X 0.0000 3 0.20 ! guess
!from methanethiol, HS S CT3 HA
!adm jr., 7/01
C CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP
! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
C CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP
! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
C N CP1 C 0.8000 3 0.00 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CA CA CA CA 3.1000 2 180.00 ! ALLOW ARO
! JES 8/25/89
CA CPT CPT CA 3.1000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
CA CT2 CT1 C 0.0400 3 0.00 ! ALLOW ARO
! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
CA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
CA NY CPT CA 3.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
CC CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CC CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
CC CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL
! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
CC CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL
! Alanine dipeptide; NMA; acetate; etc. adm jr., 3/3/93c
CD CP1 N C 0.0000 1 180.00 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CD CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL
! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
CD CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL
! Alanine dipeptide; NMA; acetate; etc. backbon adm jr., 3/3/93c
CE1 CE1 CT3 HA 0.0300 3 0.00 !
! for butene, yin/adm jr., 12/95
CE2 CE1 CT2 CT3 0.5000 1 180.00 !
! 1-butene, adm jr., 2/00 update
CE2 CE1 CT2 CT3 1.3000 3 180.00 !
! 1-butene, adm jr., 2/00 update
CE2 CE1 CT2 HA 0.1200 3 0.00 !
! for butene, yin/adm jr., 12/95
CE2 CE1 CT3 HA 0.0500 3 180.00 !
! for propene, yin/adm jr., 12/95
CP1 C N CP1 2.7500 2 180.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP1 C N CP1 0.3000 4 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 N C CP1 2.7500 2 180.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 N C CP1 0.3000 4 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 N CP1 C 0.1000 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 N CP1 CC 0.1000 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 N CP1 CP2 0.1000 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 NP CP1 C 0.0800 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CPH2 NR1 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO
! his, ADM JR., 7/20/89
CPH2 NR2 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO
! his, ADM JR., 7/20/89
CPH2 NR3 CPH1 CPH1 12.0000 2 180.00 ! ALLOW ARO
! his, ADM JR., 7/20/89
CPT CA CA CA 3.1000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
CPT CPT CA CA 3.1000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
CPT CPT CY CA 4.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
CPT CPT NY CA 5.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
CT1 C N CP1 2.7500 2 180.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT1 C N CP1 0.3000 4 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT1 C N CP3 2.7500 2 180.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT1 C N CP3 0.3000 4 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT1 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP
! Revised to adjust NMA cis/trans energy difference. (LK)
CT1 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
CT1 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP
! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
CT1 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI
! ethylbenzene ethyl rotation, adm jr. 3/7/92
CT1 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO
! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CT1 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO
! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CT1 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CT1 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO
! from ethylbenzene, adm jr., 3/7/92
CT1 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO
! from ethylbenzene, adm jr., 3/7/92
CT1 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT1 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT2 C N CP1 2.7500 2 180.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT2 C N CP1 0.3000 4 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT2 C N CP3 2.7500 2 180.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT2 C N CP3 0.3000 4 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT2 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP
! Revised to adjust NMA cis/trans energy difference. (LK)
CT2 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
CT2 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP
! Revised to adjust NMA cis/trans energy difference. (LK)
CT2 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
CT2 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP
! from CT2 C NH1 CT2, adm jr. 10/21/96
CT2 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP
! from CT2 C NH1 CT2, adm jr. 10/21/96
CT2 CA CA CA 3.1000 2 180.00 ! ALLOW ARO
! JES 8/25/89 toluene and ethylbenzene
CT2 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO
! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2
CT2 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO
! his, ADM JR., 7/22/89, FROM HA CPH1 NR2 CPH2
CT2 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90
CT2 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP
! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
CT2 CT2 CPH1 CPH1 0.4000 1 0.00 ! ALLOW ARO
! 4-methylimidazole 4-21G//6-31G* rot bar. ADM JR., 9/4/89
CT2 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI
! alkane update, adm jr., 3/2/92, butane trans/gauche
CT2 CT2 NH1 C 1.8000 1 0.00 ! ALLOW PEP
! from CT2 CT1 NH1 C, for lactams, adm jr.
CT2 CY CPT CA 3.0000 2 180.00 ! ALLOW ARO
! JWK
CT2 CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO
!JWK
CT2 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT2 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT2 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP
! Revised to adjust NMA cis/trans energy difference. (LK)
CT2 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
CT2 SM SM CT2 1.0000 1 0.00 ! ALLOW ALI SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
CT2 SM SM CT2 4.1000 2 0.00 ! ALLOW ALI SUL ION
! mp 6-311G** dimethyldisulfide, 3/26/92 (FL)
CT2 SM SM CT2 0.9000 3 0.00 ! ALLOW ALI SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
CT3 C N CP1 2.7500 2 180.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT3 C N CP1 0.3000 4 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT3 C N CP3 2.7500 2 180.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT3 C N CP3 0.3000 4 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT3 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP
! Revised to adjust NMA cis/trans energy difference. (LK)
CT3 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
CT3 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP
! for acetylated GLY N-terminus, adm jr.
CT3 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP
! for acetylated GLY N-terminus, adm jr.
CT3 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP
! Revised to adjust NMA cis/trans energy difference. (LK)
CT3 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
CT3 CA CA CA 3.1000 2 180.00 ! ALLOW ARO
! toluene, adm jr., 3/7/92
CT3 CE1 CE2 HE2 5.2000 2 180.00 !
! for propene, yin/adm jr., 12/95
CT3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO
! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2
CT3 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP
! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
CT3 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI
! ethylbenzene ethyl rotation, adm jr. 3/7/92
CT3 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO
! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CT3 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO
! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CT3 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CT3 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI
! alkane update, adm jr., 3/2/92, butane trans/gauche
CT3 CT2 CT2 CT3 0.1500 1 0.00 ! ALLOW ALI
! alkane update, adm jr., 3/2/92, butane trans/gauche
CT3 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO
! from ethylbenzene, adm jr., 3/7/92
CT3 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO
! from ethylbenzene, adm jr., 3/7/92
CT3 CT2 S CT3 0.2400 1 180.00 ! ALOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
CT3 CT2 S CT3 0.3700 3 0.00 ! ALOW ALI SUL ION
! DTN 8/24/90
CT3 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT3 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT3 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP
! Revised to adjust NMA cis/trans energy difference. (LK)
CT3 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
CT3 S CT2 CT2 0.2400 1 180.00 ! ALOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
CT3 S CT2 CT2 0.3700 3 0.00 ! ALOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
CT3 SM SM CT3 1.0000 1 0.00 ! ALLOW ALI SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
CT3 SM SM CT3 4.1000 2 0.00 ! ALLOW ALI SUL ION
! mp 6-311G** dimethyldisulfide, 3/26/92 (FL)
CT3 SM SM CT3 0.9000 3 0.00 ! ALLOW ALI SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
CY CA NY CPT 5.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
CY CPT CA CA 3.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
CY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
H NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
H NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
H NH1 C CT2 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
H NH1 C CT3 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
H NH1 CT1 C 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
H NH1 CT1 CC 0.0000 1 0.00 ! ALLOW PEP POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
H NH1 CT1 CD 0.0000 1 0.00 ! ALLOW PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
H NH1 CT1 CT1 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
H NH1 CT1 CT2 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
H NH1 CT1 CT3 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
H NH1 CT2 C 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
H NH1 CT2 CC 0.0000 1 0.00 ! ALLOW PEP POL
! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
H NH1 CT2 CD 0.0000 1 0.00 ! ALLOW PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
H NH1 CT2 CT2 0.0000 1 0.00 ! ALLOW PEP
! from H NH1 CT2 CT3, for lactams, adm jr.
H NH1 CT2 CT3 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
H NH2 CC CT1 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
! adm jr. 4/10/91, acetamide update
H NH2 CC CT2 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
! adm jr. 4/10/91, acetamide update
H NH2 CC CT3 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
! adm jr. 4/10/91, acetamide update
H NH2 CC CP1 2.5000 2 180.00 ! ALLOW PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
H NR1 CPH1 CPH1 1.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 7/20/89
H NR1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H
H NR1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H
H NR3 CPH1 CPH1 1.4000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90
H NR3 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA
H NR3 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA
H NY CA CY 0.8000 2 180.00 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
H NY CPT CA 0.8000 2 180.00 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
H NY CPT CPT 0.8000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
H OH1 CA CA 0.9900 2 180.00 ! ALLOW ARO ALC
! phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92
H OH1 CT1 CT1 1.3300 1 0.00 ! ALLOW ALC
! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT1 CT1 0.1800 2 0.00 ! ALLOW ALC
! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT1 CT1 0.3200 3 0.00 ! ALLOW ALC
! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT1 CT3 1.3300 1 0.00 ! ALLOW ALC
! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT1 CT3 0.1800 2 0.00 ! ALLOW ALC
! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT1 CT3 0.3200 3 0.00 ! ALLOW ALC
! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT1 1.3000 1 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT1 0.3000 2 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT1 0.4200 3 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT2 1.3000 1 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT2 0.3000 2 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT2 0.4200 3 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT3 1.3000 1 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT3 0.3000 2 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT3 0.4200 3 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
HA CA CA CA 3.5000 2 180.00 ! ALLOW ARO
! adm jr., 10/02/89
HA CA CA CPT 3.5000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CA CA HA 2.5000 2 180.00 ! ALLOW ARO
! ADM JR., 10/02/89
HA CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO
! TRP (JES)
HA CA CPT CY 4.0000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CA CY CPT 1.2000 2 180.00 ! ALLOW ARO
! JWK
HA CA CY CT2 1.2000 2 180.00 ! ALLOW ARO
! JWK
HA CA NY CPT 3.0000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CA NY H 1.0000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL
! adm jr. 4/10/91, acetamide update
HA CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
HA CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89
HA CT2 CY CA 0.2500 2 180.00 ! ALLOW ARO
! JWK
HA CT2 CY CPT 0.2500 2 180.00 ! ALLOW ARO
! JWK
HA CT2 NH1 C 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
HA CT2 NH1 H 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
HA CT2 S CT3 0.2800 3 0.00 ! ALLOW ALI SUL ION
! DTN 8/24/90
HA CT3 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89
HA CT3 CS HA 0.1600 3 0.00 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CT3 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
HA CT3 NH1 C 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
HA CT3 NH1 H 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
HA CT3 S CT2 0.2800 3 0.00 ! ALLOW ALI SUL ION
! DTN 8/24/90
HA CY CA CPT 1.2000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CY CA HA 1.2000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HE1 CE1 CE1 HE1 1.0000 2 180.00 !
! 2-butene, adm jr., 8/98 update
CT3 CE1 CE1 HE1 1.0000 2 180.00 !
! 2-butene, adm jr., 8/98 update
HE1 CE1 CE2 HE2 5.2000 2 180.00 !
! for propene, yin/adm jr., 12/95
HE1 CE1 CT2 HA 0.0000 3 0.00
! butene, adm jr., 2/00 update
HE1 CE1 CT2 CT3 0.1200 3 0.00 !
! for butene, yin/adm jr., 12/95
HE1 CE1 CT3 HA 0.0000 3 0.00
! butene, adm jr., 2/00 update
HE2 CE2 CE1 CT2 5.2000 2 180.00 !
! for butene, yin/adm jr., 12/95
HE2 CE2 CE1 CPB 5.2000 2 180.00 !
! for vinyl, from butene, yin/adm jr., 12/95
HB CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CP1 N CP3 0.1000 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CP1 NP CP3 0.0800 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CT1 NH1 C 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT1 NH1 H 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT2 NH1 C 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT2 NH1 H 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT3 NH1 C 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT3 NH1 H 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HC NH2 CT2 CT2 0.1100 3 0.00
!from X CT3 NH2 X, neutral lysine
HC NH2 CT2 HA 0.1100 3 0.00
!from X CT3 NH2 X, neutral lysine
HC NH2 CT2 HB 0.1100 3 0.00
!from X CT3 NH2 X, neutral glycine, adm jr.
HC NH2 CT2 CD 0.1100 3 0.00
!from X CT3 NH2 X, neutral glycine, adm jr.
HC NP CP1 C 0.0800 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HC NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HC NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HC NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HC NP CP1 HB 0.0800 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HC NP CP3 CP2 0.0800 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HC NP CP3 HA 0.0800 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HP CA CA CA 4.2000 2 180.00 ! ALLOW ARO
! JES 8/25/89 benzene
HP CA CA CPT 3.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
HP CA CA CT2 4.2000 2 180.00 ! ALLOW ARO
! JES 8/25/89 toluene and ethylbenzene
HP CA CA CT3 4.2000 2 180.00 ! ALLOW ARO
! toluene, adm jr., 3/7/92
HP CA CA HP 2.4000 2 180.00 ! ALLOW ARO
! JES 8/25/89 benzene
HP CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO
! JWK indole 05/14/91
HP CA CPT CY 3.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
HP CA CY CPT 2.0000 2 180.00 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
HP CA CY CT2 1.2000 2 180.00 ! ALLOW ARO
! JWK indole 05/14/91
HP CA NY CPT 2.0000 2 180.00 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
HP CA NY H 0.4000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
HP CY CA HP 1.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
HP CY CPT CA 2.8000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
HP CY CPT CPT 2.8000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
HR1 CPH1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90
HR1 CPH1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90
HR1 CPH1 CPH1 HR1 1.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90, his
HR1 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90
HR1 CPH1 NR3 H 3.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90
HR1 CPH2 NR1 CPH1 3.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90
HR1 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90
HR1 CPH2 NR2 CPH1 3.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90
HR2 CPH2 NR3 CPH1 3.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90
HR2 CPH2 NR3 H 0.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90, YES, 0.0
HR3 CPH1 CPH1 CT2 2.0000 2 180.00 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HR3 CPH1 CPH1 CT3 2.0000 2 180.00 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HR3 CPH1 CPH1 HR3 2.0000 2 180.00 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HR3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HR3 CPH1 NR1 H 1.0000 2 180.00 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HR3 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HS S CT2 CT1 0.2400 1 0.00 ! ALLOW ALI SUL ION
! methanethiol pure solvent, adm jr., 6/22/92
HS S CT2 CT1 0.1500 2 0.00 ! ALLOW ALI SUL ION
! methanethiol pure solvent, adm jr., 6/22/92
HS S CT2 CT1 0.2700 3 0.00 ! ALLOW ALI SUL ION
! methanethiol pure solvent, adm jr., 6/22/92
HS S CT2 CT3 0.2400 1 0.00 ! ALLOW ALI SUL ION
! ethanethiol C-C-S-H surface, adm jr., 4/18/93
HS S CT2 CT3 0.1500 2 0.00 ! ALLOW ALI SUL ION
! ethanethiol C-C-S-H surface, adm jr., 4/18/93
HS S CT2 CT3 0.2700 3 0.00 ! ALLOW ALI SUL ION
! ethanethiol C-C-S-H surface, adm jr., 4/18/93
HS S CT2 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION
! methanethiol pure solvent, adm jr., 6/22/92
HS S CT3 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION
! methanethiol pure solvent, adm jr., 6/22/92
N C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT1 HB 0.0000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT2 HB 0.0000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT3 HA 0.0000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
NH1 C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH1 C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH1 C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH1 C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH1 C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH1 C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH1 C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP
! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK)
NH1 C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP
! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK)
NH1 C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP
! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK)
NH1 C CT1 HB 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
NH1 C CT1 NH1 0.6000 1 0.00 ! ALLOW PEP
! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93
NH1 C CT2 CT2 0.0000 1 0.00 ! ALLOW PEP
! from NH1 C CT1 CT2, for lactams, adm jr.
NH1 C CT2 HA 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
NH1 C CT2 HB 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
NH1 C CT2 NH1 0.6000 1 0.00 ! ALLOW PEP
! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93
NH1 C CT3 HA 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
NH1 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH1 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH2 CC CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH2 CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH2 CC CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH2 CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH2 CC CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH2 CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH2 CC CT2 HA 0.0000 3 180.00 ! ALLOW POL
! adm jr., 8/13/90 acetamide geometry and vibrations
NH3 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH3 CT1 C NH1 0.6000 1 0.00 ! ALLOW PEP PRO
! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93
NH3 CT1 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO
! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
NH3 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH3 CT2 C NH1 0.4000 1 0.00 ! ALLOW PEP PRO
! adm jr. 3/24/92, for PRES GLYP
NH3 CT2 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO
! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
NP CP1 C N 0.3000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP1 C NH1 0.3000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP1 CC NH2 0.3000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NR1 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO
! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA
NR1 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO
! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA
NR1 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
NR1 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO
! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
NR1 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO
! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
NR1 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO
! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
NR1 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO
! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
NR1 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO
! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
NR1 CPH2 NR2 CPH1 14.0000 2 180.00 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO
! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA
NR2 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO
! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA
NR2 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
NR2 CPH1 CPH1 NR1 14.0000 2 180.00 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO
! HIS CB-CG TORSION,
NR2 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO
! HIS CB-CG TORSION,
NR2 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO
! HIS CB-CG TORSION,
NR2 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO
! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
NR2 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO
! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
NR2 CPH2 NR1 CPH1 14.0000 2 180.00 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR3 CPH1 CPH1 CT2 2.5000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90
NR3 CPH1 CPH1 CT3 2.5000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90
NR3 CPH1 CPH1 HR1 2.5000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90
NR3 CPH1 CPH1 NR3 12.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90
NR3 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO
! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
NR3 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO
! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
NR3 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO
! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
NR3 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO
! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
NR3 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO
! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
NR3 CPH2 NR3 CPH1 12.0000 2 180.00 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR3 CPH2 NR3 H 1.4000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90
NY CA CY CPT 4.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
NY CA CY CT2 3.5000 2 180.00 ! ALLOW ARO
! JWK
NY CA CY HA 3.5000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
NY CA CY HP 3.5000 2 180.00 ! ALLOW ARO
! JWK indole 05/14/91
NY CPT CA CA 2.8000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
NY CPT CA HA 4.0000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
NY CPT CA HP 3.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
NY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
NY CPT CPT CY 5.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
O C CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O C CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O C CT1 CT1 1.4000 1 0.00 ! ALLOW PEP
! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
O C CT1 CT2 1.4000 1 0.00 ! ALLOW PEP
! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
O C CT1 CT3 1.4000 1 0.00 ! ALLOW PEP
! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
O C CT1 HB 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
O C CT1 NH1 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
O C CT1 NH3 0.0000 1 0.00 ! ALLOW PEP PRO
! Backbone parameter set made complete RLD 8/8/90
O C CT2 CT2 1.4000 1 0.00 ! ALLOW PEP
! from O C CT1 CT2, for lactams, adm jr.
O C CT2 HA 0.0000 3 180.00 ! ALLOW POL
! adm jr., 8/13/90 acetamide geometry and vibrations
O C CT2 HB 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
O C CT2 NH1 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
O C CT2 NH3 0.0000 1 0.00 ! ALLOW PEP PRO
! Backbone parameter set made complete RLD 8/8/90
O C CT3 HA 0.0000 3 180.00 ! ALLOW POL
! adm jr., 8/13/90 acetamide geometry and vibrations
O C N CP1 2.7500 2 180.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O C N CP1 0.3000 4 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O C N CP3 2.7500 2 180.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O C N CP3 0.3000 4 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
O C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
O C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
O C NH1 H 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
O CC CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O CC CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O CC CT2 HA 0.0000 3 180.00 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
O CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
! adm jr. 4/10/91, acetamide update
OB CD OS CT2 0.9650 1 180.00 ! ALLOW PEP POL
! adm jr. 3/19/92, from lipid methyl acetate
OB CD OS CT2 3.8500 2 180.00 ! ALLOW PEP POL
! adm jr. 3/19/92, from lipid methyl acetate
OB CD OS CT3 0.9650 1 180.00 ! ALLOW PEP POL
! adm jr. 3/19/92, from lipid methyl acetate
OB CD OS CT3 3.8500 2 180.00 ! ALLOW PEP POL
! adm jr. 3/19/92, from lipid methyl acetate
OC CA CA CA 3.1000 2 180.00 ! ALLOW ARO
! adm jr. 8/27/91, phenoxide
OC CA CA HP 4.2000 2 180.00 ! ALLOW ARO
! adm jr. 8/27/91, phenoxide
OC CC CP1 CP2 0.1600 3 0.00 ! ALLOW PEP PRO POL
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
OC CC CP1 HB 0.1600 3 0.00 ! ALLOW PEP PRO POL
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
OC CC CP1 N 0.1600 3 0.00 ! ALLOW PEP PRO POL
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
OC CC CP1 NP 0.1600 3 0.00 ! ALLOW PEP PRO POL
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
OC CC CT1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO
! adm jr. 4/17/94, zwitterionic glycine
OC CC CT2 NH3 3.2000 2 180.00 ! ALLOW PEP PRO
! adm jr. 4/17/94, zwitterionic glycine
OH1 CA CA CA 3.1000 2 180.00 ! ALLOW ARO
! JES 8/25/89 phenol
OH1 CA CA HP 4.2000 2 180.00 ! ALLOW ARO
! JES 8/25/89 phenol
S CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION
! DTN 8/24/90
SM CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION
! DTN 8/24/90
SM SM CT2 CT1 0.3100 3 0.00 ! ALLOW SUL ALI
! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90
SM SM CT2 CT2 0.3100 3 0.00 ! ALLOW SUL ALI
! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90
SM SM CT2 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION
! expt. dimethyldisulfide, 3/26/92 (FL)
SM SM CT3 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION
! expt. dimethyldisulfide, 3/26/92 (FL)
SS CS CT3 HA 0.1500 3 0.00 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
!X C C X 4.0000 2 180.00 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
X C NC2 X 2.2500 2 180.00 ! ALLOW PEP POL ARO
! 9.0->2.25 GUANIDINIUM (KK)
X CD OH1 X 2.0500 2 180.00 ! ALLOW PEP POL ARO ALC
! adm jr, 10/17/90, acetic acid C-Oh rotation barrier
X CD OS X 2.0500 2 180.00 ! ALLOW PEP POL
! adm jr. 3/19/92, from lipid methyl acetate
X CE1 CE1 X 0.1500 1 0.00
! 2-butene, adm jr., 2/00 update
X CE1 CE1 X 8.5000 2 180.00
! 2-butene, adm jr., 2/00 update
X CE2 CE2 X 4.9000 2 180.00 !
! for ethene, yin/adm jr., 12/95
X CP1 C X 0.0000 6 180.00 ! ALLOW POL PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
X CP1 CC X 0.0000 6 180.00 ! ALLOW POL PEP
! changed to 0.0 RLD 5/19/92
X CP1 CD X 0.0000 6 180.00 ! ALLOW POL PEP
! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
X CP1 CP2 X 0.1400 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
X CP2 CP2 X 0.1600 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
X CP3 CP2 X 0.1400 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
X CPA CPB X 0.0000 2 0.00 ! ALLOW HEM
! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
X CPA CPM X 0.0000 2 0.00 ! ALLOW HEM
! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
X CPB CE1 X 3.0000 2 180.00 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
X CPB CPB X 0.0000 2 0.00 ! ALLOW HEM
! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
X CPB CT2 X 0.0000 6 0.00 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
X CPB CT3 X 0.0000 6 0.00 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
X CPT CPT X 0.0000 2 180.00 ! ALLOW ARO
! JWK indole 05/14/91
X CT1 CC X 0.0500 6 180.00 ! ALLOW POL PEP
! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
X CT1 CD X 0.0000 6 180.00 ! ALLOW POL PEP
! adm jr. 3/19/92, from lipid methyl acetate
X CT1 CT1 X 0.2000 3 0.00 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL
! 0.715->0.10 METHYLAMMONIUM (KK)
X CT1 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO
! EMB 11/21/89 methanol vib fit
X CT1 OS X -0.1000 3 0.00 ! ALLOW PEP POL
! adm jr. 3/19/92, from lipid methyl acetate
X CT2 CA X 0.0000 6 0.00 ! ALLOW ALI ARO
! toluene, adm jr., 3/7/92
X CT2 CC X 0.0500 6 180.00 ! ALLOW POL PEP
! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
X CT2 CD X 0.0000 6 180.00 ! ALLOW POL PEP
! adm jr. 3/19/92, from lipid methyl acetate
X CT2 CT2 X 0.1950 3 0.00 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
X CT2 CT3 X 0.1600 3 0.00 ! ALLOW ALI
! rotation barrier in Ethane (SF)
X CT2 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL
! methylguanidinium, adm jr., 3/26/92
X CT2 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL
! 0.715->0.10 METHYLAMMONIUM (KK)
X CT2 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO
! EMB 11/21/89 methanol vib fit
X CT2 OS X -0.1000 3 0.00 ! ALLOW PEP POL
! adm jr. 3/19/92, from lipid methyl acetate
X CT3 CA X 0.0000 6 0.00 ! ALLOW ALI ARO
! toluene, adm jr., 3/7/92
X CT3 CC X 0.0500 6 180.00 ! ALLOW POL PEP
! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
X CT3 CD X 0.0000 6 180.00 ! ALLOW POL PEP
! adm jr. 3/19/92, from lipid methyl acetate
X CT3 CT3 X 0.1550 3 0.00 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
X CT3 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL
! methylguanidinium, adm jr., 3/26/92
X CT3 NH2 X 0.1100 3 0.00 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
X CT3 NH3 X 0.0900 3 0.00 ! ALLOW ALI POL
! fine-tuned to ab initio; METHYLAMMONIUM, KK 03/10/92
X CT3 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO
! EMB 11/21/89 methanol vib fit
X CT3 OS X -0.1000 3 0.00 ! ALLOW PEP POL
! adm jr. 3/19/92, from lipid methyl acetate
X FE CM X 0.0500 4 0.00 ! ALLOW HEM
! Heme (6-liganded): ligands (KK 05/13/91)
X FE NPH X 0.0000 2 0.00 ! ALLOW HEM
! Heme (6-liganded): for "ic para" only (KK 05/13/91)
X FE NR2 X 0.0500 4 0.00 ! ALLOW HEM
! Heme (6-liganded): from param19.inp
X FE OM X 0.0000 4 0.00 ! ALLOW HEM
! Heme (6-liganded): ligands (KK 05/13/91)
X NPH CPA X 0.0000 2 0.00 ! ALLOW HEM
! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
IMPROPER
!
!V(improper) = Kpsi(psi - psi0)**2
!
!Kpsi: kcal/mole/rad**2
!psi0: degrees
!note that the second column of numbers (0) is ignored
!
!atom types Kpsi psi0
!
CPB CPA NPH CPA 20.8000 0 0.0000 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB X X CE1 90.0000 0 0.0000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT2 X X CPB 90.0000 0 0.0000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT3 X X CPB 90.0000 0 0.0000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
!HA C C HA 20.0000 0 0.0000 ! ALLOW PEP POL ARO
! Heme vinyl substituent (KK, from propene (JCS))
HA CPA CPA CPM 29.4000 0 0.0000 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
!HA CPB C C 20.0000 0 0.0000 ! ALLOW HEM ARO
! Heme (6-liganded): substituents (KK 05/13/91)
!HA HA C C 20.0000 0 180.0000 ! ALLOW PEP POL ARO
! Heme vinyl substituent (KK, from propene (JCS))
HE2 HE2 CE2 CE2 3.0 0 0.00 !
! for ethene, yin/adm jr., 12/95
HR1 NR1 NR2 CPH2 0.5000 0 0.0000 ! ALLOW ARO
! his, adm jr., 7/05/90
HR1 NR2 NR1 CPH2 0.5000 0 0.0000 ! ALLOW ARO
! his, adm jr., 7/05/90
HR3 CPH1 NR1 CPH1 0.5000 0 0.0000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HR3 CPH1 NR2 CPH1 0.5000 0 0.0000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HR3 CPH1 NR3 CPH1 1.0000 0 0.0000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HR3 NR1 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HR3 NR2 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
N C CP1 CP3 0.0000 0 0.0000 ! ALLOW PRO
! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92
NC2 X X C 40.0000 0 0.0000 ! ALLOW PEP POL ARO
! 5.75->40.0 GUANIDINIUM (KK)
NH1 X X H 20.0000 0 0.0000 ! ALLOW PEP POL ARO
! NMA Vibrational Modes (LK)
NH2 X X H 4.0000 0 0.0000 ! ALLOW POL
! adm jr., 8/13/90 acetamide geometry and vibrations
NPH CPA CPA FE 137.4000 0 0.0000 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH CPA CPB CPB 40.6000 0 0.0000 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH CPA CPM CPA 18.3000 0 0.0000 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH CPM CPB CPA 32.7000 0 0.0000 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NR1 CPH1 CPH2 H 0.4500 0 0.0000 ! ALLOW ARO
! his, adm jr., 7/05/90
NR1 CPH2 CPH1 H 0.4500 0 0.0000 ! ALLOW ARO
! his, adm jr., 7/05/90
NR3 CPH1 CPH2 H 1.2000 0 0.0000 ! ALLOW ARO
! his, adm jr., 6/27/90
NR3 CPH2 CPH1 H 1.2000 0 0.0000 ! ALLOW ARO
! his, adm jr., 6/27/90
NY CA CY CPT 100.0000 0 0.0000 ! ALLOW ARO
!adm jr., 5/15/91, indole 3-21G HE1 out-of-plane surf.
O CP1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO
! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92
O CT1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL
! adm jr., 8/13/90 acetamide geometry and vibrations
O CT2 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL
! adm jr., 8/13/90 acetamide geometry and vibrations
O CT3 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL
! adm jr., 8/13/90 acetamide geometry and vibrations
O HA NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO
! adm jr., 5/13/91, formamide geometry and vibrations
O N CT2 CC 120.0000 0 0.0000 ! ALLOW PEP POL PRO
! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92
O NH2 CP1 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO
! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92
O NH2 CT1 CC 45.0000 0 0.0000 ! ALLOW PEP POL
! adm jr., 8/13/90 acetamide geometry and vibrations
O NH2 CT2 CC 45.0000 0 0.0000 ! ALLOW PEP POL
! adm jr., 8/13/90 acetamide geometry and vibrations
O NH2 CT3 CC 45.0000 0 0.0000 ! ALLOW PEP POL
! adm jr., 8/13/90 acetamide geometry and vibrations
O NH2 HA CC 45.0000 0 0.0000 ! ALLOW PEP POL
! adm jr., 5/13/91, formamide geometry and vibrations
O X X C 120.0000 0 0.0000 ! ALLOW PEP POL ARO
! NMA Vibrational Modes (LK)
OB X X CD 100.0000 0 0.0000 ! ALLOW ALC ARO POL
! adm jr., 10/17/90, acetic acid vibrations
OC X X CC 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
! 90.0->96.0 acetate, single impr (KK)
CC X X CT1 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
! 90.0->96.0 acetate, single impr (KK)
CC X X CT2 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
! 90.0->96.0 acetate, single impr (KK)
CC X X CT3 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
! 90.0->96.0 acetate, single impr (KK)
CMAP
! 2D grid correction data. The following surfaces are the correction
! to the CHARMM22 phi, psi alanine, proline and glycine dipeptide surfaces.
! Use of CMAP requires generation with the topology file containing the
! CMAP specifications along with version 31 or later of CHARMM. Note that
! use of "skip CMAP" yields the charmm22 energy surfaces.
!
! references
!MacKerell, A.D., Jr., Feig, M., Brooks, C.L., III, Accurate Treatment of
!Protein Backbone Conformational Energetics in Empirical Force Fields, Submitted
!for publication.
!MacKerell, A.D., Jr., Feig, M., Brooks, C.L., III, Improved Treatment of the
!Protein Backbone in Empirical Force Fields, Journal of the American Chemical
!Society, In Press.
! alanine map
C NH1 CT1 C NH1 CT1 C NH1 24
!-180
0.126790 0.768700 0.971260 1.250970 2.121010
2.695430 2.064440 1.764790 0.755870 -0.713470
0.976130 -2.475520 -5.455650 -5.096450 -5.305850
-3.975630 -3.088580 -2.784200 -2.677120 -2.646060
-2.335350 -2.010440 -1.608040 -0.482250
!-165
-0.802290 1.377090 1.577020 1.872290 2.398990
2.461630 2.333840 1.904070 1.061460 0.518400
-0.116320 -3.575440 -5.284480 -5.160310 -4.196010
-3.276210 -2.715340 -1.806200 -1.101780 -1.210320
-1.008810 -0.637100 -1.603360 -1.776870
!-150
-0.634810 1.156210 1.624350 2.047200 2.653910
2.691410 2.296420 1.960450 1.324930 2.038290
-1.151510 -3.148610 -4.058280 -4.531850 -3.796370
-2.572090 -1.727250 -0.961410 -0.282910 -0.479120
-1.039340 -1.618060 -1.725460 -1.376360
!-135
0.214000 1.521370 1.977440 2.377950 2.929470
2.893410 2.435810 2.162970 1.761500 1.190090
-1.218610 -2.108900 -2.976100 -3.405340 -2.768440
-1.836030 -0.957950 0.021790 -0.032760 -0.665880
-1.321170 -1.212320 -0.893170 -0.897040
!-120
0.873950 1.959160 2.508990 2.841100 3.698960
3.309330 2.614300 2.481720 2.694660 1.082440
-0.398320 -1.761800 -2.945110 -3.294690 -2.308300
-0.855480 -0.087320 0.439040 0.691880 -0.586330
-1.027210 -0.976640 -0.467580 0.104020
!-105
1.767380 2.286650 2.818030 3.065500 3.370620
3.397440 2.730310 2.878790 2.542010 1.545240
-0.092150 -1.694440 -2.812310 -2.802430 -1.856360
-0.306240 -0.122440 0.444680 0.810150 -0.058630
-0.270290 -0.178830 0.202360 0.493810
!-90
1.456010 2.743180 2.589450 3.046230 3.451510
3.319160 3.052900 3.873720 2.420650 0.949100
0.008370 -1.382980 -2.138930 -2.087380 -1.268300
-0.494370 0.267580 0.908250 0.537520 0.306260
0.069540 0.097460 0.263060 0.603220
!-75
1.396790 3.349090 2.180920 2.942960 3.814070
3.675800 3.555310 3.887290 2.101260 -0.190940
-0.732240 -1.382040 -0.673880 -0.817390 -0.826980
-0.111800 0.053710 0.296400 0.692240 0.428960
-0.036100 -0.033820 -0.194300 0.400210
!-60
0.246650 1.229980 1.716960 3.168570 4.208190
4.366860 4.251080 3.348110 0.997540 -1.287540
-1.179900 -0.684300 -0.853660 -1.158760 -0.347550
0.114810 0.242800 0.322420 0.370140 -0.374950
-0.676940 -1.323430 -1.366650 -0.218770
!-45
-1.196730 0.078060 2.347410 4.211350 5.376000
5.364940 4.355200 2.436510 0.408470 -0.590840
-0.435960 -0.501210 -0.822230 -0.607210 0.057910
0.246580 -0.070570 0.379430 0.247770 -0.571680
-1.282910 -1.715770 -1.839820 -1.987110
!-30
-1.174720 1.067030 4.180460 6.741610 6.070770
4.781470 2.758340 1.295810 0.571150 -0.196480
0.251860 -0.732140 1.289360 1.497590 1.890550
2.198490 0.169290 0.534000 0.331780 -1.276320
-2.550070 -3.312150 -3.136670 -2.642260
!-15
0.293590 5.588070 3.732620 3.217620 3.272450
2.492320 1.563700 1.356760 0.831410 0.630170
1.591970 0.821920 0.486070 0.715760 0.996020
1.591580 -0.367400 0.181770 -0.613920 -2.267900
-3.516460 -3.597700 -3.043340 -1.765020
!0
2.832310 0.787990 0.323280 0.479230 0.628600
0.976330 1.238750 1.671950 1.645480 2.520340
1.606970 0.776350 0.119780 0.070390 0.121170
-1.569230 -1.213010 -1.846360 -2.744510 -3.792530
-3.934880 -3.615930 -2.675750 -0.924170
!15
-0.778340 -1.912680 -2.052140 -1.846280 -1.047430
0.183400 1.682950 2.223500 1.358370 2.448660
1.436920 0.678570 -0.237060 -0.535320 -0.790380
-2.182580 -3.251140 -4.195110 -4.269270 -3.908210
-3.455620 -2.773970 1.755370 0.313410
!30
-2.963810 -3.483730 -3.517080 -2.724860 -1.405510
0.336200 1.428450 1.394630 0.970370 2.462720
1.522430 0.553620 -0.407380 -1.482950 -3.613920
-4.159810 -4.945580 -4.784040 -3.764540 -2.959140
-1.963850 -1.071260 -1.599580 -2.445320
!45
-4.029070 -3.932660 -3.558480 -2.513980 -1.037320
0.362000 0.814380 0.754110 0.502370 1.903420
0.770220 -0.416420 -3.286310 -3.875270 -4.907800
-5.704430 -5.645660 -4.396040 -2.865450 -2.368170
-2.860490 -3.416560 -3.666490 -3.859070
!60
-3.338270 -2.960220 -2.311700 -1.272890 -0.246470
0.722610 0.668070 0.438130 2.395330 1.632470
-2.041450 -3.218100 -3.915080 -4.852510 -5.696500
-6.314370 -5.683690 -4.170620 -3.141000 -3.508820
-3.756430 -3.640810 -3.640430 -3.550690
!75
-2.244860 -1.632100 -1.000640 -0.170440 0.526440
0.823710 0.517140 -0.013120 -0.370910 -1.213720
-2.305650 -3.420580 -4.484960 -5.693140 -6.199150
-6.253870 -5.211310 -4.174380 -3.685150 -4.151360
-4.161970 -3.725150 -3.715310 -2.606760
!90
-1.720840 -1.177830 -0.428430 0.277730 0.807900
0.803260 0.482510 -0.336900 -0.786270 -1.774070
-2.793220 -3.828560 -5.211800 -6.636850 -6.989940
-6.108800 -5.452410 -3.911450 -4.321000 -4.587240
-4.102610 -3.772820 -3.157300 -2.648390
!105
-1.850640 -1.092420 -0.445020 0.128490 1.005520
0.884820 0.485850 -0.218470 -0.857670 -1.682330
-3.014400 -4.481110 -6.053510 -6.865400 -6.871130
-5.728240 -3.912230 -4.802110 -5.034640 -4.715990
-4.601080 -4.086220 -3.274630 -2.410940
!120
-1.969230 -1.116650 -0.540250 -0.150330 0.763520
1.038890 0.758480 0.313530 -0.333050 -1.872770
-3.366270 -5.008260 -6.124810 -7.034830 -6.724320
-3.700200 -4.510620 -5.185650 -5.361620 -4.847490
-4.444320 -4.004260 -3.415720 -2.751230
!135
-2.111250 -1.168960 -0.322790 -0.006920 0.316660
1.086270 0.939170 0.625340 -0.166360 -1.830310
-3.469470 -4.946030 -6.112560 -1.915580 -4.047310
-4.996740 -4.996730 -4.842690 -4.886620 -4.300540
-4.494620 -4.442210 -4.163570 -3.183510
!150
-1.757590 -0.403620 0.023920 0.362390 0.634520
1.264920 1.361360 0.948420 -0.073680 -1.483560
-3.152820 1.835120 -1.762860 -5.093660 -5.744830
-5.390070 -4.783930 -4.190630 -4.115420 -4.042280
-4.125570 -4.028550 -4.026100 -2.937910
!165
-0.810590 -0.071500 0.378890 0.543310 1.277880
1.641310 1.698840 1.519950 0.631950 -1.088670
-2.736530 -0.735240 -4.563830 -6.408350 -5.889450
-5.141750 -4.194970 -3.666490 -3.843450 -3.818830
-3.826180 -3.596820 -2.994790 -2.231020
! alanine before proline map
C NH1 CT1 C NH1 CT1 C N 24
!-180
0.126790 0.768700 0.971260 1.250970 2.121010
2.695430 2.064440 1.764790 0.755870 -0.713470
0.976130 -2.475520 -5.455650 -5.096450 -5.305850
-3.975630 -3.088580 -2.784200 -2.677120 -2.646060
-2.335350 -2.010440 -1.608040 -0.482250
!-165
-0.802290 1.377090 1.577020 1.872290 2.398990
2.461630 2.333840 1.904070 1.061460 0.518400
-0.116320 -3.575440 -5.284480 -5.160310 -4.196010
-3.276210 -2.715340 -1.806200 -1.101780 -1.210320
-1.008810 -0.637100 -1.603360 -1.776870
!-150
-0.634810 1.156210 1.624350 2.047200 2.653910
2.691410 2.296420 1.960450 1.324930 2.038290
-1.151510 -3.148610 -4.058280 -4.531850 -3.796370
-2.572090 -1.727250 -0.961410 -0.282910 -0.479120
-1.039340 -1.618060 -1.725460 -1.376360
!-135
0.214000 1.521370 1.977440 2.377950 2.929470
2.893410 2.435810 2.162970 1.761500 1.190090
-1.218610 -2.108900 -2.976100 -3.405340 -2.768440
-1.836030 -0.957950 0.021790 -0.032760 -0.665880
-1.321170 -1.212320 -0.893170 -0.897040
!-120
0.873950 1.959160 2.508990 2.841100 3.698960
3.309330 2.614300 2.481720 2.694660 1.082440
-0.398320 -1.761800 -2.945110 -3.294690 -2.308300
-0.855480 -0.087320 0.439040 0.691880 -0.586330
-1.027210 -0.976640 -0.467580 0.104020
!-105
1.767380 2.286650 2.818030 3.065500 3.370620
3.397440 2.730310 2.878790 2.542010 1.545240
-0.092150 -1.694440 -2.812310 -2.802430 -1.856360
-0.306240 -0.122440 0.444680 0.810150 -0.058630
-0.270290 -0.178830 0.202360 0.493810
!-90
1.456010 2.743180 2.589450 3.046230 3.451510
3.319160 3.052900 3.873720 2.420650 0.949100
0.008370 -1.382980 -2.138930 -2.087380 -1.268300
-0.494370 0.267580 0.908250 0.537520 0.306260
0.069540 0.097460 0.263060 0.603220
!-75
1.396790 3.349090 2.180920 2.942960 3.814070
3.675800 3.555310 3.887290 2.101260 -0.190940
-0.732240 -1.382040 -0.673880 -0.817390 -0.826980
-0.111800 0.053710 0.296400 0.692240 0.428960
-0.036100 -0.033820 -0.194300 0.400210
!-60
0.246650 1.229980 1.716960 3.168570 4.208190
4.366860 4.251080 3.348110 0.997540 -1.287540
-1.179900 -0.684300 -0.853660 -1.158760 -0.347550
0.114810 0.242800 0.322420 0.370140 -0.374950
-0.676940 -1.323430 -1.366650 -0.218770
!-45
-1.196730 0.078060 2.347410 4.211350 5.376000
5.364940 4.355200 2.436510 0.408470 -0.590840
-0.435960 -0.501210 -0.822230 -0.607210 0.057910
0.246580 -0.070570 0.379430 0.247770 -0.571680
-1.282910 -1.715770 -1.839820 -1.987110
!-30
-1.174720 1.067030 4.180460 6.741610 6.070770
4.781470 2.758340 1.295810 0.571150 -0.196480
0.251860 -0.732140 1.289360 1.497590 1.890550
2.198490 0.169290 0.534000 0.331780 -1.276320
-2.550070 -3.312150 -3.136670 -2.642260
!-15
0.293590 5.588070 3.732620 3.217620 3.272450
2.492320 1.563700 1.356760 0.831410 0.630170
1.591970 0.821920 0.486070 0.715760 0.996020
1.591580 -0.367400 0.181770 -0.613920 -2.267900
-3.516460 -3.597700 -3.043340 -1.765020
!0
2.832310 0.787990 0.323280 0.479230 0.628600
0.976330 1.238750 1.671950 1.645480 2.520340
1.606970 0.776350 0.119780 0.070390 0.121170
-1.569230 -1.213010 -1.846360 -2.744510 -3.792530
-3.934880 -3.615930 -2.675750 -0.924170
!15
-0.778340 -1.912680 -2.052140 -1.846280 -1.047430
0.183400 1.682950 2.223500 1.358370 2.448660
1.436920 0.678570 -0.237060 -0.535320 -0.790380
-2.182580 -3.251140 -4.195110 -4.269270 -3.908210
-3.455620 -2.773970 1.755370 0.313410
!30
-2.963810 -3.483730 -3.517080 -2.724860 -1.405510
0.336200 1.428450 1.394630 0.970370 2.462720
1.522430 0.553620 -0.407380 -1.482950 -3.613920
-4.159810 -4.945580 -4.784040 -3.764540 -2.959140
-1.963850 -1.071260 -1.599580 -2.445320
!45
-4.029070 -3.932660 -3.558480 -2.513980 -1.037320
0.362000 0.814380 0.754110 0.502370 1.903420
0.770220 -0.416420 -3.286310 -3.875270 -4.907800
-5.704430 -5.645660 -4.396040 -2.865450 -2.368170
-2.860490 -3.416560 -3.666490 -3.859070
!60
-3.338270 -2.960220 -2.311700 -1.272890 -0.246470
0.722610 0.668070 0.438130 2.395330 1.632470
-2.041450 -3.218100 -3.915080 -4.852510 -5.696500
-6.314370 -5.683690 -4.170620 -3.141000 -3.508820
-3.756430 -3.640810 -3.640430 -3.550690
!75
-2.244860 -1.632100 -1.000640 -0.170440 0.526440
0.823710 0.517140 -0.013120 -0.370910 -1.213720
-2.305650 -3.420580 -4.484960 -5.693140 -6.199150
-6.253870 -5.211310 -4.174380 -3.685150 -4.151360
-4.161970 -3.725150 -3.715310 -2.606760
!90
-1.720840 -1.177830 -0.428430 0.277730 0.807900
0.803260 0.482510 -0.336900 -0.786270 -1.774070
-2.793220 -3.828560 -5.211800 -6.636850 -6.989940
-6.108800 -5.452410 -3.911450 -4.321000 -4.587240
-4.102610 -3.772820 -3.157300 -2.648390
!105
-1.850640 -1.092420 -0.445020 0.128490 1.005520
0.884820 0.485850 -0.218470 -0.857670 -1.682330
-3.014400 -4.481110 -6.053510 -6.865400 -6.871130
-5.728240 -3.912230 -4.802110 -5.034640 -4.715990
-4.601080 -4.086220 -3.274630 -2.410940
!120
-1.969230 -1.116650 -0.540250 -0.150330 0.763520
1.038890 0.758480 0.313530 -0.333050 -1.872770
-3.366270 -5.008260 -6.124810 -7.034830 -6.724320
-3.700200 -4.510620 -5.185650 -5.361620 -4.847490
-4.444320 -4.004260 -3.415720 -2.751230
!135
-2.111250 -1.168960 -0.322790 -0.006920 0.316660
1.086270 0.939170 0.625340 -0.166360 -1.830310
-3.469470 -4.946030 -6.112560 -1.915580 -4.047310
-4.996740 -4.996730 -4.842690 -4.886620 -4.300540
-4.494620 -4.442210 -4.163570 -3.183510
!150
-1.757590 -0.403620 0.023920 0.362390 0.634520
1.264920 1.361360 0.948420 -0.073680 -1.483560
-3.152820 1.835120 -1.762860 -5.093660 -5.744830
-5.390070 -4.783930 -4.190630 -4.115420 -4.042280
-4.125570 -4.028550 -4.026100 -2.937910
!165
-0.810590 -0.071500 0.378890 0.543310 1.277880
1.641310 1.698840 1.519950 0.631950 -1.088670
-2.736530 -0.735240 -4.563830 -6.408350 -5.889450
-5.141750 -4.194970 -3.666490 -3.843450 -3.818830
-3.826180 -3.596820 -2.994790 -2.231020
! proline
C N CP1 C N CP1 C NH1 24
! -180.00
-4.60660 -4.28920 -4.51420 -5.49210 -6.65460
-7.18530 -7.63320 -8.41920 -9.12510 -8.97830
-9.02750 -8.88890 -8.61060 -8.10240 -7.96680
-7.98860 -7.96190 -7.56330 -7.73950 -8.31580
-9.33380 -9.61880 -7.91860 -6.00570
! -165.00
-3.21030 -2.90350 -3.04340 -3.83720 -4.92360
-5.41790 -5.78320 -6.62490 -7.17820 -7.59500
-7.60980 -7.39440 -6.68190 -6.24950 -5.83810
-5.90510 -5.57900 -4.89950 -5.18840 -6.13180
-6.93510 -7.49160 -5.84410 -4.48890
! -150.00
-2.23750 -2.26520 -2.55120 -3.67610 -4.61620
-5.01560 -5.36920 -5.93110 -6.16820 -6.48830
-6.54220 -6.14310 -5.33350 -4.85090 -4.50790
-4.44050 -4.34380 -4.13820 -4.35620 -5.24880
-6.05280 -6.18610 -4.80390 -3.41730
! -135.00
-2.12830 -2.02010 -2.90220 -3.88240 -4.63610
-5.02000 -5.46090 -5.79830 -5.63220 -6.41490
-6.20330 -5.57550 -4.58160 -4.15850 -4.00710
-3.95020 -3.76880 -4.09690 -4.52680 -5.33410
-5.97380 -5.68710 -4.70040 -3.33790
! -120.00
-2.20610 -2.22370 -2.85110 -3.55370 -4.33320
-4.57860 -4.95030 -5.23950 -5.37730 -6.14740
-5.98660 -5.17760 -4.16090 -3.78450 -3.83210
-3.86590 -4.21340 -4.26250 -4.16200 -4.62160
-5.47440 -5.38280 -4.39100 -3.16760
! -105.00
-1.32980 -1.44660 -2.00420 -2.84440 -3.31580
-3.15410 -2.83060 -3.04980 -4.04810 -5.02030
-4.84090 -3.88520 -2.79540 -2.49190 -2.65990
-3.34670 -3.60580 -3.76970 -4.07430 -4.21930
-4.66740 -4.23940 -3.37160 -2.10050
! -90.00
-0.27400 -0.41780 -0.92340 -1.48470 -1.84370
-1.42480 -1.14210 -1.83280 -2.97900 -3.57000
-3.33310 -2.24200 -1.31350 -0.96640 0.38300
-0.57540 -0.74080 -0.59130 -0.41960 -2.64120
-3.25380 -2.85540 -2.09970 -0.95660
! -75.00
0.26880 0.18190 0.00300 -0.45390 -0.24210
0.21240 0.33320 -0.95520 -2.17670 -2.66490
-2.24910 -1.35480 -0.35030 1.84000 0.81880
0.41530 0.58460 0.65350 0.54960 0.41300
0.23350 -2.13490 -1.54900 -0.38340
! -60.00
-0.48820 -0.40730 -0.25210 -0.20490 0.53370
1.05990 0.72540 -0.68300 -2.10190 -2.83530
-2.55500 -1.33940 -0.24710 1.63190 1.10600
1.16350 1.30720 1.49310 1.16160 0.99320
-2.33360 -2.59380 -2.01110 -1.46840
! -45.00
-2.41010 -1.30740 -0.85960 -0.06830 0.20500
0.00650 -0.59750 -2.39820 -3.98270 -4.46610
-3.51230 -1.99330 0.96050 0.80870 0.64450
0.82590 1.00550 1.28110 0.96670 -2.71140
-4.18330 -4.83370 -4.49950 -3.47920
! -30.00
-3.46300 -2.06680 -0.84260 -0.70440 -1.85140
-2.59990 -3.62600 -5.08050 -6.35480 -6.08340
-4.78650 -1.24210 -0.81660 -0.60170 -0.50040
-0.41020 -0.28450 -0.14620 -3.14950 -5.16280
-6.81940 -7.52060 -7.12480 -5.49420
! -15.00
-2.70550 -1.11410 -0.82120 -3.80470 -4.50780
-4.64960 -5.78530 -7.04450 -7.30810 -6.56450
-3.47860 -2.68630 -1.78120 -1.48400 -1.45930
-1.43060 -5.75320 -2.72500 -6.45790 -8.16530
-9.86330 -9.80710 -8.62670 -6.49690
! 0.00
-2.73190 -3.83060 -5.26960 -5.91610 -6.71690
-7.05420 -7.77520 -7.81220 -7.54160 -4.98400
-5.05070 -4.28910 -3.78740 -3.64600 -3.91990
-3.55740 -3.03470 -5.78910 -7.02720 -8.04090
-8.60950 -8.27740 -7.10120 -5.12040
! 15.00
-3.17420 -4.66830 -6.17790 -7.26760 -8.22560
-8.32120 -7.64880 -7.00240 -4.77210 -5.65380
-5.36790 -4.43640 -4.37720 -4.45280 -4.47980
-4.07260 -6.75420 -7.56910 -7.95830 -7.87760
-7.88160 -7.29010 -7.15600 -5.19260
! 30.00
-2.96240 -4.87720 -6.64930 -7.95180 -8.47610
-7.49950 -6.26260 -6.35040 -4.34190 -4.49790
-4.27480 -1.75620 -3.89990 -3.81400 -3.99610
-6.66430 -7.66400 -7.80660 -7.21980 -6.83750
-6.88220 -7.10200 -5.10200 -2.38920
!45
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
!60
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
!75
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
!90
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
!105
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
!120
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
!135
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
!150
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
!165
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
!2 adjacent prolines
C N CP1 C N CP1 C N 24
! -180.00
-4.60660 -4.28920 -4.51420 -5.49210 -6.65460
-7.18530 -7.63320 -8.41920 -9.12510 -8.97830
-9.02750 -8.88890 -8.61060 -8.10240 -7.96680
-7.98860 -7.96190 -7.56330 -7.73950 -8.31580
-9.33380 -9.61880 -7.91860 -6.00570
! -165.00
-3.21030 -2.90350 -3.04340 -3.83720 -4.92360
-5.41790 -5.78320 -6.62490 -7.17820 -7.59500
-7.60980 -7.39440 -6.68190 -6.24950 -5.83810
-5.90510 -5.57900 -4.89950 -5.18840 -6.13180
-6.93510 -7.49160 -5.84410 -4.48890
! -150.00
-2.23750 -2.26520 -2.55120 -3.67610 -4.61620
-5.01560 -5.36920 -5.93110 -6.16820 -6.48830
-6.54220 -6.14310 -5.33350 -4.85090 -4.50790
-4.44050 -4.34380 -4.13820 -4.35620 -5.24880
-6.05280 -6.18610 -4.80390 -3.41730
! -135.00
-2.12830 -2.02010 -2.90220 -3.88240 -4.63610
-5.02000 -5.46090 -5.79830 -5.63220 -6.41490
-6.20330 -5.57550 -4.58160 -4.15850 -4.00710
-3.95020 -3.76880 -4.09690 -4.52680 -5.33410
-5.97380 -5.68710 -4.70040 -3.33790
! -120.00
-2.20610 -2.22370 -2.85110 -3.55370 -4.33320
-4.57860 -4.95030 -5.23950 -5.37730 -6.14740
-5.98660 -5.17760 -4.16090 -3.78450 -3.83210
-3.86590 -4.21340 -4.26250 -4.16200 -4.62160
-5.47440 -5.38280 -4.39100 -3.16760
! -105.00
-1.32980 -1.44660 -2.00420 -2.84440 -3.31580
-3.15410 -2.83060 -3.04980 -4.04810 -5.02030
-4.84090 -3.88520 -2.79540 -2.49190 -2.65990
-3.34670 -3.60580 -3.76970 -4.07430 -4.21930
-4.66740 -4.23940 -3.37160 -2.10050
! -90.00
-0.27400 -0.41780 -0.92340 -1.48470 -1.84370
-1.42480 -1.14210 -1.83280 -2.97900 -3.57000
-3.33310 -2.24200 -1.31350 -0.96640 0.38300
-0.57540 -0.74080 -0.59130 -0.41960 -2.64120
-3.25380 -2.85540 -2.09970 -0.95660
! -75.00
0.26880 0.18190 0.00300 -0.45390 -0.24210
0.21240 0.33320 -0.95520 -2.17670 -2.66490
-2.24910 -1.35480 -0.35030 1.84000 0.81880
0.41530 0.58460 0.65350 0.54960 0.41300
0.23350 -2.13490 -1.54900 -0.38340
! -60.00
-0.48820 -0.40730 -0.25210 -0.20490 0.53370
1.05990 0.72540 -0.68300 -2.10190 -2.83530
-2.55500 -1.33940 -0.24710 1.63190 1.10600
1.16350 1.30720 1.49310 1.16160 0.99320
-2.33360 -2.59380 -2.01110 -1.46840
! -45.00
-2.41010 -1.30740 -0.85960 -0.06830 0.20500
0.00650 -0.59750 -2.39820 -3.98270 -4.46610
-3.51230 -1.99330 0.96050 0.80870 0.64450
0.82590 1.00550 1.28110 0.96670 -2.71140
-4.18330 -4.83370 -4.49950 -3.47920
! -30.00
-3.46300 -2.06680 -0.84260 -0.70440 -1.85140
-2.59990 -3.62600 -5.08050 -6.35480 -6.08340
-4.78650 -1.24210 -0.81660 -0.60170 -0.50040
-0.41020 -0.28450 -0.14620 -3.14950 -5.16280
-6.81940 -7.52060 -7.12480 -5.49420
! -15.00
-2.70550 -1.11410 -0.82120 -3.80470 -4.50780
-4.64960 -5.78530 -7.04450 -7.30810 -6.56450
-3.47860 -2.68630 -1.78120 -1.48400 -1.45930
-1.43060 -5.75320 -2.72500 -6.45790 -8.16530
-9.86330 -9.80710 -8.62670 -6.49690
! 0.00
-2.73190 -3.83060 -5.26960 -5.91610 -6.71690
-7.05420 -7.77520 -7.81220 -7.54160 -4.98400
-5.05070 -4.28910 -3.78740 -3.64600 -3.91990
-3.55740 -3.03470 -5.78910 -7.02720 -8.04090
-8.60950 -8.27740 -7.10120 -5.12040
! 15.00
-3.17420 -4.66830 -6.17790 -7.26760 -8.22560
-8.32120 -7.64880 -7.00240 -4.77210 -5.65380
-5.36790 -4.43640 -4.37720 -4.45280 -4.47980
-4.07260 -6.75420 -7.56910 -7.95830 -7.87760
-7.88160 -7.29010 -7.15600 -5.19260
! 30.00
-2.96240 -4.87720 -6.64930 -7.95180 -8.47610
-7.49950 -6.26260 -6.35040 -4.34190 -4.49790
-4.27480 -1.75620 -3.89990 -3.81400 -3.99610
-6.66430 -7.66400 -7.80660 -7.21980 -6.83750
-6.88220 -7.10200 -5.10200 -2.38920
!45
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
!60
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
!75
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
!90
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
!105
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
!120
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
!135
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
!150
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
!165
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
! glycine map
C NH1 CT2 C NH1 CT2 C NH1 24
!-180
-0.549160 -0.535500 -0.588110 -0.754620 -0.679290
-0.038150 0.298460 0.326040 -0.375610 -1.704360
-3.061280 -3.956460 -3.576280 -1.038930 2.012450
-1.714610 -0.377660 0.317310 0.294580 -0.042920
-0.676620 -0.744600 -0.586590 -0.554770
!-165
-0.709450 -0.896700 -0.990850 -1.319240 -0.940260
-0.126160 0.329180 0.258100 -0.534910 -1.715700
-2.780320 -3.153350 -1.636020 1.822690 -2.675640
-1.810120 -0.410680 0.180860 0.196710 -0.000430
-0.271890 -0.462500 -0.348750 -0.477660
!-150
-1.224850 -1.482430 -1.665900 -1.656770 -1.119780
-1.642540 -0.054220 -0.290670 -0.887080 -1.626260
-2.165440 -1.546500 0.753400 -2.949180 -2.225630
-1.664160 -0.628990 0.000490 0.033160 -0.092820
-0.339050 -0.563330 -0.794980 -0.710760
!-135
-1.787640 -2.117750 -2.143020 -1.803720 -1.567160
-0.886880 -0.801350 -0.851590 -1.020630 -1.337360
-1.062570 0.338010 -4.372310 -2.435890 -2.220710
-1.718060 -0.758950 -0.207560 0.100910 -0.055650
-0.288370 -0.880610 -1.267450 -1.465530
!-120
-2.348270 -2.593790 -2.596140 -2.364070 -1.970070
-1.705860 -1.435540 -1.289220 -1.358170 -0.975570
-3.514390 -4.283210 -3.975820 -3.215190 -2.394430
-1.455320 -0.553910 -0.158900 -0.173830 -0.297950
-0.661220 -1.068330 -1.601800 -1.914850
!-105
-2.788800 -3.079570 -3.178150 -3.013710 -2.626630
-2.266680 -1.951490 -1.681850 -1.195390 -2.567680
-3.632800 -4.748210 -4.662850 -4.255190 -2.776760
-1.695490 -0.893140 -0.633810 -0.467320 -0.540540
-0.950190 -1.401500 -1.959970 -2.412680
!-90
-3.857170 -3.713610 -3.902110 -3.611370 -3.040850
-2.406460 -1.975250 -1.452040 -0.971860 -2.808170
-4.181160 -4.981430 -5.446890 -4.359900 -2.864390
-1.898510 -1.139090 -0.971340 -1.065550 -1.020680
-1.141350 -1.794480 -2.420970 -2.939990
!-75
-4.987770 -4.995210 -4.485310 -3.892550 -3.228630
-2.345360 -1.664160 -1.105500 -1.945510 -3.715530
-4.492140 -5.536170 -5.708500 -3.675410 -2.986660
-1.859410 -0.756620 -1.269930 -1.312730 -1.607440
-1.892510 -2.659400 -3.347950 -3.970600
!-60
-6.183650 -5.456080 -4.878940 -4.000820 -2.683230
-2.067520 -1.094850 -1.119790 -2.962910 -3.687830
-4.993340 -4.666260 -3.796280 -3.374140 -2.495430
-1.453990 -0.877560 -1.002930 -1.337310 -2.431360
-2.948140 -4.008100 -4.821040 -5.565810
!-45
-6.755760 -5.850030 -4.362190 -2.714090 -1.708710
-0.526660 -0.536700 -2.037170 -3.892650 -4.558570
-4.237410 -3.735160 -3.688580 -3.009910 -2.112940
-1.455400 -0.925490 -1.121840 -1.561900 -2.751370
-4.094860 -5.207530 -6.128530 -6.613030
!-30
-5.716250 -4.434060 -2.788600 -0.974400 -0.729200
-0.904940 -1.833540 -3.017700 -3.313450 -3.336010
-3.181640 -3.594720 -1.231370 -0.603790 0.128810
-1.222610 -0.909150 -0.837700 -1.346820 -3.040880
-4.731110 -5.844860 -6.428460 -6.424880
!-15
-3.991110 -2.046000 0.082550 -2.676110 -2.828500
-2.596640 -2.843330 -3.011480 -2.312640 -2.405980
-3.086210 -1.164620 -1.231660 -0.871900 -0.348980
-1.735900 -0.914150 -0.484520 -1.818040 -3.602550
-5.330320 -5.992270 -5.588080 -5.408360
!0
-1.147060 -3.317730 -4.305100 -4.615200 -4.533780
-3.622950 -2.832800 -1.872810 -1.144300 -1.994070
-0.741980 -1.115010 -1.229250 -1.103680 -0.742430
-1.973970 -1.070020 -1.802220 -2.712770 -3.624130
-4.537100 -4.619970 -4.310890 -3.318290
!15
-3.997710 -5.408360 -5.588080 -5.992270 -5.330320
-3.602550 -1.818040 -0.484520 -0.914150 -1.735900
-0.348980 -0.871900 -1.231660 -1.164620 -3.086210
-2.405980 -2.312640 -3.011480 -2.843330 -2.596640
-2.828500 -2.676110 0.082550 -2.046000
!30
-5.710850 -6.424880 -6.428460 -5.844860 -4.731110
-3.040880 -1.346820 -0.837700 -0.909150 -1.222610
0.128810 -0.603790 -1.231370 -3.594720 -3.181640
-3.336010 -3.313450 -3.017700 -1.833540 -0.904940
-0.729200 -0.974400 -2.788600 -4.434060
!45
-6.754940 -6.613030 -6.128530 -5.207530 -4.094860
-2.751370 -1.561900 -1.121840 -0.925490 -1.455400
-2.112940 -3.009910 -3.688580 -3.735160 -4.237410
-4.558570 -3.892650 -2.037170 -0.536700 -0.526660
-1.708710 -2.714090 -4.362190 -5.850030
!60
-6.188070 -5.565810 -4.821040 -4.008100 -2.948140
-2.431360 -1.337310 -1.002930 -0.877560 -1.453990
-2.495430 -3.374140 -3.796280 -4.666260 -4.993340
-3.687830 -2.962910 -1.119790 -1.094850 -2.067520
-2.683230 -4.000820 -4.878940 -5.456080
!75
-4.986080 -3.970600 -3.347950 -2.659400 -1.892510
-1.607440 -1.312730 -1.269930 -0.756620 -1.859410
-2.986660 -3.675410 -5.708500 -5.536170 -4.492140
-3.715530 -1.945510 -1.105500 -1.664160 -2.345360
-3.228630 -3.892550 -4.485310 -4.995210
!90
-3.879190 -2.939990 -2.420970 -1.794480 -1.141350
-1.020680 -1.065550 -0.971340 -1.139090 -1.898510
-2.864390 -4.359900 -5.446890 -4.981430 -4.181160
-2.808170 -0.971860 -1.452040 -1.975250 -2.406460
-3.040850 -3.611370 -3.902110 -3.713610
!105
-2.793280 -2.412680 -1.959970 -1.401500 -0.950190
-0.540540 -0.467320 -0.633810 -0.893140 -1.695490
-2.776760 -4.255190 -4.662850 -4.448210 -3.332800
-2.567680 -1.195390 -1.681850 -1.951490 -2.266680
-2.626630 -3.013710 -3.178150 -3.079570
!120
-2.330190 -1.914850 -1.601800 -1.068330 -0.661220
-0.297950 -0.173830 -0.158900 -0.553910 -1.455320
-2.394430 -3.215190 -3.975820 -3.783210 -3.014390
-0.975570 -1.358170 -1.289220 -1.435540 -1.705860
-1.970070 -2.364070 -2.596140 -2.593790
!135
-1.796120 -1.465530 -1.267450 -0.880610 -0.288370
-0.055650 0.100910 -0.207560 -0.758950 -1.718060
-2.220710 -2.435890 -4.372310 0.338010 -1.062570
-1.337360 -1.020630 -0.851590 -0.801350 -0.886880
-1.567160 -1.803720 -2.143020 -2.117750
!150
-1.263610 -0.710760 -0.794980 -0.563330 -0.339050
-0.092820 0.033160 0.000490 -0.628990 -1.664160
-2.225630 -2.949180 0.753400 -1.546500 -2.165440
-1.626260 -0.887080 -0.290670 -0.054220 -1.642540
-1.119780 -1.656770 -1.665900 -1.482430
!165
-0.684660 -0.477660 -0.348750 -0.462500 -0.271890
-0.000430 0.196710 0.180860 -0.410680 -1.810120
-2.675640 1.822690 -1.636020 -3.153350 -2.780320
-1.715700 -0.534910 0.258100 0.329180 -0.126160
-0.940260 -1.319240 -0.990850 -0.896700
! glycine before proline map: use glycine map
C NH1 CT2 C NH1 CT2 C N 24
!-180
-0.549160 -0.535500 -0.588110 -0.754620 -0.679290
-0.038150 0.298460 0.326040 -0.375610 -1.704360
-3.061280 -3.956460 -3.576280 -1.038930 2.012450
-1.714610 -0.377660 0.317310 0.294580 -0.042920
-0.676620 -0.744600 -0.586590 -0.554770
!-165
-0.709450 -0.896700 -0.990850 -1.319240 -0.940260
-0.126160 0.329180 0.258100 -0.534910 -1.715700
-2.780320 -3.153350 -1.636020 1.822690 -2.675640
-1.810120 -0.410680 0.180860 0.196710 -0.000430
-0.271890 -0.462500 -0.348750 -0.477660
!-150
-1.224850 -1.482430 -1.665900 -1.656770 -1.119780
-1.642540 -0.054220 -0.290670 -0.887080 -1.626260
-2.165440 -1.546500 0.753400 -2.949180 -2.225630
-1.664160 -0.628990 0.000490 0.033160 -0.092820
-0.339050 -0.563330 -0.794980 -0.710760
!-135
-1.787640 -2.117750 -2.143020 -1.803720 -1.567160
-0.886880 -0.801350 -0.851590 -1.020630 -1.337360
-1.062570 0.338010 -4.372310 -2.435890 -2.220710
-1.718060 -0.758950 -0.207560 0.100910 -0.055650
-0.288370 -0.880610 -1.267450 -1.465530
!-120
-2.348270 -2.593790 -2.596140 -2.364070 -1.970070
-1.705860 -1.435540 -1.289220 -1.358170 -0.975570
-3.514390 -4.283210 -3.975820 -3.215190 -2.394430
-1.455320 -0.553910 -0.158900 -0.173830 -0.297950
-0.661220 -1.068330 -1.601800 -1.914850
!-105
-2.788800 -3.079570 -3.178150 -3.013710 -2.626630
-2.266680 -1.951490 -1.681850 -1.195390 -2.567680
-3.632800 -4.748210 -4.662850 -4.255190 -2.776760
-1.695490 -0.893140 -0.633810 -0.467320 -0.540540
-0.950190 -1.401500 -1.959970 -2.412680
!-90
-3.857170 -3.713610 -3.902110 -3.611370 -3.040850
-2.406460 -1.975250 -1.452040 -0.971860 -2.808170
-4.181160 -4.981430 -5.446890 -4.359900 -2.864390
-1.898510 -1.139090 -0.971340 -1.065550 -1.020680
-1.141350 -1.794480 -2.420970 -2.939990
!-75
-4.987770 -4.995210 -4.485310 -3.892550 -3.228630
-2.345360 -1.664160 -1.105500 -1.945510 -3.715530
-4.492140 -5.536170 -5.708500 -3.675410 -2.986660
-1.859410 -0.756620 -1.269930 -1.312730 -1.607440
-1.892510 -2.659400 -3.347950 -3.970600
!-60
-6.183650 -5.456080 -4.878940 -4.000820 -2.683230
-2.067520 -1.094850 -1.119790 -2.962910 -3.687830
-4.993340 -4.666260 -3.796280 -3.374140 -2.495430
-1.453990 -0.877560 -1.002930 -1.337310 -2.431360
-2.948140 -4.008100 -4.821040 -5.565810
!-45
-6.755760 -5.850030 -4.362190 -2.714090 -1.708710
-0.526660 -0.536700 -2.037170 -3.892650 -4.558570
-4.237410 -3.735160 -3.688580 -3.009910 -2.112940
-1.455400 -0.925490 -1.121840 -1.561900 -2.751370
-4.094860 -5.207530 -6.128530 -6.613030
!-30
-5.716250 -4.434060 -2.788600 -0.974400 -0.729200
-0.904940 -1.833540 -3.017700 -3.313450 -3.336010
-3.181640 -3.594720 -1.231370 -0.603790 0.128810
-1.222610 -0.909150 -0.837700 -1.346820 -3.040880
-4.731110 -5.844860 -6.428460 -6.424880
!-15
-3.991110 -2.046000 0.082550 -2.676110 -2.828500
-2.596640 -2.843330 -3.011480 -2.312640 -2.405980
-3.086210 -1.164620 -1.231660 -0.871900 -0.348980
-1.735900 -0.914150 -0.484520 -1.818040 -3.602550
-5.330320 -5.992270 -5.588080 -5.408360
!0
-1.147060 -3.317730 -4.305100 -4.615200 -4.533780
-3.622950 -2.832800 -1.872810 -1.144300 -1.994070
-0.741980 -1.115010 -1.229250 -1.103680 -0.742430
-1.973970 -1.070020 -1.802220 -2.712770 -3.624130
-4.537100 -4.619970 -4.310890 -3.318290
!15
-3.997710 -5.408360 -5.588080 -5.992270 -5.330320
-3.602550 -1.818040 -0.484520 -0.914150 -1.735900
-0.348980 -0.871900 -1.231660 -1.164620 -3.086210
-2.405980 -2.312640 -3.011480 -2.843330 -2.596640
-2.828500 -2.676110 0.082550 -2.046000
!30
-5.710850 -6.424880 -6.428460 -5.844860 -4.731110
-3.040880 -1.346820 -0.837700 -0.909150 -1.222610
0.128810 -0.603790 -1.231370 -3.594720 -3.181640
-3.336010 -3.313450 -3.017700 -1.833540 -0.904940
-0.729200 -0.974400 -2.788600 -4.434060
!45
-6.754940 -6.613030 -6.128530 -5.207530 -4.094860
-2.751370 -1.561900 -1.121840 -0.925490 -1.455400
-2.112940 -3.009910 -3.688580 -3.735160 -4.237410
-4.558570 -3.892650 -2.037170 -0.536700 -0.526660
-1.708710 -2.714090 -4.362190 -5.850030
!60
-6.188070 -5.565810 -4.821040 -4.008100 -2.948140
-2.431360 -1.337310 -1.002930 -0.877560 -1.453990
-2.495430 -3.374140 -3.796280 -4.666260 -4.993340
-3.687830 -2.962910 -1.119790 -1.094850 -2.067520
-2.683230 -4.000820 -4.878940 -5.456080
!75
-4.986080 -3.970600 -3.347950 -2.659400 -1.892510
-1.607440 -1.312730 -1.269930 -0.756620 -1.859410
-2.986660 -3.675410 -5.708500 -5.536170 -4.492140
-3.715530 -1.945510 -1.105500 -1.664160 -2.345360
-3.228630 -3.892550 -4.485310 -4.995210
!90
-3.879190 -2.939990 -2.420970 -1.794480 -1.141350
-1.020680 -1.065550 -0.971340 -1.139090 -1.898510
-2.864390 -4.359900 -5.446890 -4.981430 -4.181160
-2.808170 -0.971860 -1.452040 -1.975250 -2.406460
-3.040850 -3.611370 -3.902110 -3.713610
!105
-2.793280 -2.412680 -1.959970 -1.401500 -0.950190
-0.540540 -0.467320 -0.633810 -0.893140 -1.695490
-2.776760 -4.255190 -4.662850 -4.448210 -3.332800
-2.567680 -1.195390 -1.681850 -1.951490 -2.266680
-2.626630 -3.013710 -3.178150 -3.079570
!120
-2.330190 -1.914850 -1.601800 -1.068330 -0.661220
-0.297950 -0.173830 -0.158900 -0.553910 -1.455320
-2.394430 -3.215190 -3.975820 -3.783210 -3.014390
-0.975570 -1.358170 -1.289220 -1.435540 -1.705860
-1.970070 -2.364070 -2.596140 -2.593790
!135
-1.796120 -1.465530 -1.267450 -0.880610 -0.288370
-0.055650 0.100910 -0.207560 -0.758950 -1.718060
-2.220710 -2.435890 -4.372310 0.338010 -1.062570
-1.337360 -1.020630 -0.851590 -0.801350 -0.886880
-1.567160 -1.803720 -2.143020 -2.117750
!150
-1.263610 -0.710760 -0.794980 -0.563330 -0.339050
-0.092820 0.033160 0.000490 -0.628990 -1.664160
-2.225630 -2.949180 0.753400 -1.546500 -2.165440
-1.626260 -0.887080 -0.290670 -0.054220 -1.642540
-1.119780 -1.656770 -1.665900 -1.482430
!165
-0.684660 -0.477660 -0.348750 -0.462500 -0.271890
-0.000430 0.196710 0.180860 -0.410680 -1.810120
-2.675640 1.822690 -1.636020 -3.153350 -2.780320
-1.715700 -0.534910 0.258100 0.329180 -0.126160
-0.940260 -1.319240 -0.990850 -0.896700
NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
!adm jr., 5/08/91, suggested cutoff scheme
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
!
!carbons
C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO
! NMA pure solvent, adm jr., 3/3/93
CA 0.000000 -0.070000 1.992400 ! ALLOW ARO
! benzene (JES)
CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO
! adm jr. 3/3/92, acetic acid heat of solvation
CD 0.000000 -0.070000 2.000000 ! ALLOW POL
! adm jr. 3/19/92, acetate a.i. and dH of solvation
CE1 0.000000 -0.068000 2.090000 !
! for propene, yin/adm jr., 12/95
CE2 0.000000 -0.064000 2.080000 !
! for ethene, yin/adm jr., 12/95
CM 0.000000 -0.110000 2.100000 ! ALLOW HEM
! Heme (6-liganded): CO ligand carbon (KK 05/13/91)
CP1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CP2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CPA 0.000000 -0.090000 1.800000 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB 0.000000 -0.090000 1.800000 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPH1 0.000000 -0.050000 1.800000 ! ALLOW ARO
! adm jr., 10/23/91, imidazole solvation and sublimation
CPH2 0.000000 -0.050000 1.800000 ! ALLOW ARO
! adm jr., 10/23/91, imidazole solvation and sublimation
CPM 0.000000 -0.090000 1.800000 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPT 0.000000 -0.090000 1.800000 0.000000 -0.090000 1.900000 ! ALLOW ARO
! benzene (JES)
CS 0.000000 -0.110000 2.200000 ! ALLOW SUL
! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92
CST 0.000000 -0.058000 1.563000 !
! carbon dioxide, JES
CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI
! isobutane pure solvent properties, adm jr, 2/3/92
CT2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI
! propane pure solvent properties, adm jr, 2/3/92
CT3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI
! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92
CY 0.000000 -0.070000 1.992400 ! ALLOW ARO
! TRP, JWK 08/29/89
!new alkanes atoms types for conversion to new LJ parameters for c27 (see toppar_all22_prot_aliphatic_c27.str)
CT 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! from CT1x: needs work
CT1x 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! alkane, 3/92: needs work
CT2x 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
CT3x 0.0 -0.0780 2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
! hydrogens
H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC
! same as TIP3P hydrogen, adm jr., 7/20/89
HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC
! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92
HE1 0.000000 -0.031000 1.250000 !
! for propene, yin/adm jr., 12/95
HE2 0.000000 -0.026000 1.260000 !
! for ethene, yin/adm jr., 12/95
HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC
! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92
HC 0.000000 -0.046000 0.224500 ! ALLOW POL
! new, small polar Hydrogen, see also adm jr. JG 8/27/89
HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! ALLOW ARO
! JES 8/25/89 values from Jorgensen fit to hydration energy
HR1 0.000000 -0.046000 0.900000 ! ALLOW ARO
! adm jr., 6/27/90, his
HR2 0.000000 -0.046000 0.700000 ! ALLOW ARO
! adm jr., 6/27/90, his
HR3 0.000000 -0.007800 1.468000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HS 0.000000 -0.100000 0.450000 ! ALLOW SUL
! methanethiol pure solvent, adm jr., 6/22/92
HT 0.000000 -0.046000 0.224500 ! ALLOW WAT
!TIP3P HYDROGEN PARAMETERS, adm jr., NBFIX obsolete
!new alkanes atoms types for conversion to new LJ parameters for c27 (see toppar_all22_prot_aliphatic_c27.str)
HA1 0.0 -0.022 1.3200 ! alkane, 3/92
HA2 0.0 -0.028 1.3400 ! alkane, yin and mackerell, 4/98
HA3 0.0 -0.024 1.3400 ! alkane, yin and mackerell, 4/98
!nitrogens
N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC2 0.000000 -0.200000 1.850000 ! ALLOW POL
! JG 8/27/89; note: NH1 in ARG was changed to NC2.
NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO
! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK)
NH2 0.000000 -0.200000 1.850000 ! ALLOW POL
! adm jr.
NH3 0.000000 -0.200000 1.850000 ! ALLOW POL
! adm jr.
NP 0.000000 -0.200000 1.850000 ! ALLOW PRO
! N-terminal proline; from 6-31g* +ProNH2 RLD 9/28/90
NPH 0.000000 -0.200000 1.850000 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NR1 0.000000 -0.200000 1.850000 ! ALLOW ARO
! His, adm jr., 9/4/89
NR2 0.000000 -0.200000 1.850000 ! ALLOW ARO
! His, adm jr., 9/4/89
NR3 0.000000 -0.200000 1.850000 ! ALLOW ARO
! His, adm jr., 9/4/89
NY 0.000000 -0.200000 1.850000 ! ALLOW ARO
! trp, JWK
! oxygens
O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL
! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK)
OB 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ARO
! adm jr., 10/17/90, acetic acid carbonyl O
OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION
! JG 8/27/89
OH1 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO
! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P)
OM 0.000000 -0.120000 1.700000 ! ALLOW HEM
! Heme (6-liganded): CO ligand oxygen (KK 05/13/91)
OS 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO
! adm jr. 9/17/90, avoid O* wildcard
OST 0.000000 -0.165000 1.692000 !
! carbon dioxide, JES
OT 0.000000 -0.152100 1.768200 ! ALLOW WAT
!TIP3P OXYGEN PARAMETERS, adm jr., NBFIX obsolete
! sulfurs
S 0.000000 -0.450000 2.000000 ! ALLOW SUL ION
! adm jr., 3/3/92, methanethiol/ethylmethylsulfide pure solvent
SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION
! adm jr., 3/3/92, dimethyldisulphide pure solvent
SS 0.000000 -0.470000 2.200000 ! ALLOW SUL
! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92
! ions and miscellaneous types
SOD 0.0 -0.0469 1.36375 ! sodium
! D. Beglovd and B. Roux, dA=-100.8 kcal/mol
POT 0.0 -0.0870 1.76375 ! potassium
! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol
CLA 0.0 -0.150 2.27 ! chloride
! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol
CAL 0.0 -0.120 1.367 ! Calcium
! S. Marchand and B. Roux, dA = -384.8 kcal/mol
!CAL 0.000000 -0.120000 1.710000 ! Calcium (BP) in proteins prior
! to 2003; not recommended due to need for NBFIX terms
MG 0.0 -0.0150 1.18500 ! Magnesium
! B. Roux dA = -441.65
CES 0.0 -0.1900 2.100
! Cesium, so far untested.
ZN 0.000000 -0.250000 1.090000 ! ALLOW ION
! RHS March 18, 1990
FE 0.010000 0.000000 0.650000 ! ALLOW HEM
! Heme (6-liganded): Iron atom (KK 05/13/91)
HE 0.000000 -0.021270 1.4800 !
! helium, experimental pot. energy surface, adm jr., 12/95
NE 0.000000 -0.086000 1.5300
! neon, semiempirical pot. energy surface, adm jr., 12/95
CLAL 0.000000 -0.030000 1.908200 ! chlorine from Jorgensen/BOSS
! for choroacetaldehyde
DUM 0.000000 -0.000000 0.000000 !
! dummy atom
!pyridine series LJ parametes (see toppar_pyridines.str)
CAP 0.000000 -0.070000 1.992400 !
FA 0.000000 -0.12000 1.700000
! from 1,3-difluorobenzene pure solvent
CN 0.000000 -0.200000 1.750000 ! cyanopyridine
NC 0.000000 -0.600000 1.850000 ! cyanopyridine
OCA 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! 3acp
COA 0.000000 -0.110000 2.000000 ! 3acp
!fluorinated alkanes LJ parameters (see toppar_fluoro_alkanes.str)
CF1 0.000000 -0.060000 1.900000
CF2 0.000000 -0.042000 2.050000
CF3 0.000000 -0.020000 2.300000
HF1 0.000000 -0.028000 1.3200
HF2 0.000000 -0.030000 1.3000
F1 0.0 -0.135 1.63
F2 0.0 -0.105 1.63
F3 0.0 -0.097 1.60
!protein model compounds (see toppar_all22_prot_model.str)
C3 0.000000 -0.020000 2.275000 ! cyclopropane, JMW and CBP 4/04
!retinol model compounds
CC1A 0.0 -0.0680 2.0900 !
CC1B 0.0 -0.0680 2.0900 !
CC2 0.0 -0.0640 2.0800 !
NS1 0.000000 -0.200000 1.850000 !N for deprotonated Schiff's base
NS2 0.000000 -0.200000 1.850000 !N for protonated Schiff's base
HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use
! READ PARAM APPEND CARD
! to append hbond parameters from the file: par_hbond.inp
END
examples/charmm22.rtf 0 → 100644
View file @ cc97a0ba
*>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
*>>>>>>>>>>>>>>>>>>>>>> December, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
* All comments to ADM jr. via the CHARMM web site: www.charmm.org
* parameter set discussion forum
*
31 1
! 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.
!
!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)
!
MASS 1 H 1.00800 H ! polar H
MASS 2 HC 1.00800 H ! N-ter H
MASS 3 HA 1.00800 H ! nonpolar H
MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN
MASS 5 HP 1.00800 H ! aromatic H
MASS 6 HB 1.00800 H ! backbone H
MASS 7 HR1 1.00800 H ! his he1, (+) his HG,HD2
MASS 8 HR2 1.00800 H ! (+) his HE1
MASS 9 HR3 1.00800 H ! neutral his HG, HD2
MASS 10 HS 1.00800 H ! thiol hydrogen
MASS 11 HE1 1.00800 H ! for alkene; RHC=CR
MASS 12 HE2 1.00800 H ! for alkene; H2C=CR
MASS 13 HA1 1.00800 H ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS 14 HA2 1.00800 H ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS 15 HA3 1.00800 H ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS 16 HF1 1.00800 H ! Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str)
MASS 17 HF2 1.00800 H ! Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str)
MASS 20 C 12.01100 C ! carbonyl C, peptide backbone
MASS 21 CA 12.01100 C ! aromatic C
MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH
MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2
MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3
MASS 25 CPH1 12.01100 C ! his CG and CD2 carbons
MASS 26 CPH2 12.01100 C ! his CE1 carbon
MASS 27 CPT 12.01100 C ! trp C between rings
MASS 28 CY 12.01100 C ! TRP C in pyrrole ring
MASS 29 CP1 12.01100 C ! tetrahedral C (proline CA)
MASS 30 CP2 12.01100 C ! tetrahedral C (proline CB/CG)
MASS 31 CP3 12.01100 C ! tetrahedral C (proline CD)
MASS 32 CC 12.01100 C ! carbonyl C, asn,asp,gln,glu,cter,ct2
MASS 33 CD 12.01100 C ! carbonyl C, pres aspp,glup,ct1
MASS 34 CPA 12.01100 C ! heme alpha-C
MASS 35 CPB 12.01100 C ! heme beta-C
MASS 36 CPM 12.01100 C ! heme meso-C
MASS 37 CM 12.01100 C ! heme CO carbon
MASS 38 CS 12.01100 C ! thiolate carbon
MASS 39 CE1 12.01100 C ! for alkene; RHC=CR
MASS 40 CE2 12.01100 C ! for alkene; H2C=CR
MASS 41 CST 12.01100 C ! CO2 carbon
MASS 42 CT 12.01100 C ! aliphatic sp3 C, new LJ params, no hydrogens (see toppar_all22_prot_aliphatic_c27.str)
MASS 43 CT1x 12.01100 C ! aliphatic sp3 C for CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS 44 CT2x 12.01100 C ! aliphatic sp3 C for CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS 45 CT3x 12.01100 C ! aliphatic sp3 C for CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS 46 CN 12.01100 C ! C for cyano group (see toppar_all22_prot_pyridines.str)
MASS 47 CAP 12.01100 C ! aromatic C for pyrimidines (see toppar_all22_prot_pyridines.str)
MASS 48 COA 12.01100 C ! carbonyl C for pyrimidines (see toppar_all22_prot_pyridines.str)
MASS 49 C3 12.01100 C ! cyclopropyl carbon
MASS 50 N 14.00700 N ! proline N
MASS 51 NR1 14.00700 N ! neutral his protonated ring nitrogen
MASS 52 NR2 14.00700 N ! neutral his unprotonated ring nitrogen
MASS 53 NR3 14.00700 N ! charged his ring nitrogen
MASS 54 NH1 14.00700 N ! peptide nitrogen
MASS 55 NH2 14.00700 N ! amide nitrogen
MASS 56 NH3 14.00700 N ! ammonium nitrogen
MASS 57 NC2 14.00700 N ! guanidinium nitroogen
MASS 58 NY 14.00700 N ! TRP N in pyrrole ring
MASS 59 NP 14.00700 N ! Proline ring NH2+ (N-terminal)
MASS 60 NPH 14.00700 N ! heme pyrrole N
MASS 61 NC 14.00700 N ! N for cyano group (see toppar_all22_prot_pyridines.str)
MASS 70 O 15.99900 O ! carbonyl oxygen
MASS 71 OB 15.99900 O ! carbonyl oxygen in acetic acid
MASS 72 OC 15.99900 O ! carboxylate oxygen
MASS 73 OH1 15.99900 O ! hydroxyl oxygen
MASS 74 OS 15.99940 O ! ester oxygen
MASS 75 OT 15.99940 O ! TIPS3P WATER OXYGEN
MASS 76 OM 15.99900 O ! heme CO/O2 oxygen
MASS 77 OST 15.99900 O ! CO2 oxygen
MASS 78 OCA 15.99900 O ! carbonyl O for pyrimidines (see toppar_all22_prot_pyridines.str)
MASS 81 S 32.06000 S ! sulphur
MASS 82 SM 32.06000 S ! sulfur C-S-S-C type
MASS 83 SS 32.06000 S ! thiolate sulfur
MASS 85 HE 4.00260 HE ! helium
MASS 86 NE 20.17970 NE ! neon
MASS 87 CF1 12.01100 C ! monofluoromethyl (see toppar_all22_prot_fluoro_alkanes.str)
MASS 88 CF2 12.01100 C ! difluoromethyl (see toppar_all22_prot_fluoro_alkanes.str)
MASS 89 CF3 12.01100 C ! trifluoromethyl (see toppar_all22_prot_fluoro_alkanes.str)
MASS 90 FE 55.84700 Fe ! heme iron 56
MASS 91 CLAL 35.45300 CL ! Chlorine Atom (see toppar_all22_prot_aldehydes.str)
MASS 92 FA 18.99800 F ! aromatic flourine (see toppar_all22_prot_pyridines.str)
MASS 93 F1 18.99800 F ! Fluorine, monofluoro (see toppar_all22_prot_fluoro_alkanes.str)
MASS 94 F2 18.99800 F ! Fluorine, difluoro (see toppar_all22_prot_fluoro_alkanes.str)
MASS 95 F3 18.99800 F ! Fluorine, trifluoro (see toppar_all22_prot_fluoro_alkanes.str)
MASS 99 DUM 0.00000 H ! dummy atom
MASS 100 SOD 22.989770 NA ! Sodium Ion
MASS 101 MG 24.305000 MG ! Magnesium Ion
MASS 102 POT 39.102000 K ! Potassium Ion! check masses
MASS 103 CES 132.900000 CS ! Cesium Ion
MASS 104 CAL 40.080000 CA ! Calcium Ion
MASS 105 CLA 35.450000 CL ! Chloride Ion
MASS 106 ZN 65.370000 ZN ! zinc (II) cation
!the following masses must be added to the parent RTF for retinol/al
MASS 112 CC1A 12.01100 C ! alkene conjugation
MASS 113 CC1B 12.01100 C ! alkene conjugation
MASS 114 CC2 12.01100 C ! alkene conjugation
MASS 120 NS1 14.00700 N ! N for deprotonated Schiff's base
MASS 121 NS2 14.00700 N ! N for protonated Schiff's base
DECL -CA
DECL -C
DECL -O
DECL +N
DECL +HN
DECL +CA
DEFA FIRS NTER LAST CTER
AUTO ANGLES DIHE
RESI ALA 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1
ATOM HA HB 0.09 ! | /
GROUP ! HA-CA--CB-HB2
ATOM CB CT3 -0.27 ! | \
ATOM HB1 HA 0.09 ! | HB3
ATOM HB2 HA 0.09 ! O=C
ATOM HB3 HA 0.09 ! |
GROUP !
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA N HN N CA
BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3
DOUBLE O C
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
DONOR HN N
ACCEPTOR O C
IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996
IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390
IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558
IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297
IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613
IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461
IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840
IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109
IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119
IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114
RESI ARG 1.00
GROUP
ATOM N NH1 -0.47 ! | HH11
ATOM HN H 0.31 ! HN-N |
ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE NH1-HH12
ATOM HA HB 0.09 ! | | | | | //(+)
GROUP ! HA-CA--CB--CG--CD--NE--CZ
ATOM CB CT2 -0.18 ! | | | | \
ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 NH2-HH22
ATOM HB2 HA 0.09 ! O=C |
GROUP ! | HH21
ATOM CG CT2 -0.18
ATOM HG1 HA 0.09
ATOM HG2 HA 0.09
GROUP
ATOM CD CT2 0.20
ATOM HD1 HA 0.09
ATOM HD2 HA 0.09
ATOM NE NC2 -0.70
ATOM HE HC 0.44
ATOM CZ C 0.64
ATOM NH1 NC2 -0.80
ATOM HH11 HC 0.46
ATOM HH12 HC 0.46
ATOM NH2 NC2 -0.80
ATOM HH21 HC 0.46
ATOM HH22 HC 0.46
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD CG NE CD CZ NE
BOND NH2 CZ N HN N CA
BOND C CA C +N CA HA CB HB1
BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2
BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22
DOUBLE O C CZ NH1
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
IMPR CZ NH1 NH2 NE
DONOR HN N
DONOR HE NE
DONOR HH11 NH1
DONOR HH12 NH1
DONOR HH21 NH2
DONOR HH22 NH2
ACCEPTOR O C
IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973
IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227
IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511
IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271
IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565
IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552
IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836
IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475
IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163
IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124
IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384
IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121
IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143
IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034
IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143
IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150
IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401
IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065
IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311
IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903
IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023
IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292
IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899
IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914
RESI ASN 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 OD1 HD21 (cis to OD1)
ATOM HA HB 0.09 ! | | || /
GROUP ! HA-CA--CB--CG--ND2
ATOM CB CT2 -0.18 ! | | \
ATOM HB1 HA 0.09 ! | HB2 HD22 (trans to OD1)
ATOM HB2 HA 0.09 ! O=C
GROUP ! |
ATOM CG CC 0.55
ATOM OD1 O -0.55
GROUP
ATOM ND2 NH2 -0.62
ATOM HD21 H 0.32
ATOM HD22 H 0.30
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB ND2 CG
BOND N HN N CA C CA C +N
BOND CA HA CB HB1 CB HB2 ND2 HD21 ND2 HD22
DOUBLE C O CG OD1
IMPR N -C CA HN C CA +N O
IMPR CG ND2 CB OD1 CG CB ND2 OD1
IMPR ND2 CG HD21 HD22 ND2 CG HD22 HD21
CMAP -C N CA C N CA C +N
DONOR HN N
DONOR HD21 ND2
DONOR HD22 ND2
ACCEPTOR OD1 CG
ACCEPTOR O C
IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992
IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245
IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467
IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282
IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528
IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627
IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848
IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319
IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120
IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091
IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323
IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521
IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963
IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951
RESI ASP -1.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 OD1
ATOM HA HB 0.09 ! | | //
GROUP ! HA-CA--CB--CG
ATOM CB CT2 -0.28 ! | | \
ATOM HB1 HA 0.09 ! | HB2 OD2(-)
ATOM HB2 HA 0.09 ! O=C
ATOM CG CC 0.62 ! |
ATOM OD1 OC -0.76
ATOM OD2 OC -0.76
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB OD2 CG
BOND N HN N CA C CA C +N
BOND CA HA CB HB1 CB HB2
DOUBLE O C CG OD1
IMPR N -C CA HN C CA +N O
!IMPR OD1 CB OD2 CG
IMPR CG CB OD2 OD1
CMAP -C N CA C N CA C +N
DONOR HN N
ACCEPTOR OD1 CG
ACCEPTOR OD2 CG
ACCEPTOR O C
IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966
IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315
IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478
IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330
IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484
IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619
IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841
IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218
IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086
IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080
IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565
IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541
RESI CYS 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1
ATOM HA HB 0.09 ! | |
GROUP ! HA-CA--CB--SG
ATOM CB CT2 -0.11 ! | | \
ATOM HB1 HA 0.09 ! | HB2 HG1
ATOM HB2 HA 0.09 ! O=C
ATOM SG S -0.23 ! |
ATOM HG1 HS 0.16
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA SG CB N HN N CA
BOND C CA C +N CA HA CB HB1
BOND CB HB2 SG HG1
DOUBLE O C
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
DONOR HN N
DONOR HG1 SG
ACCEPTOR O C
IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982
IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202
IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498
IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306
IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548
IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584
IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837
IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359
IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134
IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124
IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341
RESI GLN 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 HG1 OE1 HE21 (cis to OE1)
ATOM HA HB 0.09 ! | | | || /
GROUP ! HA-CA--CB--CG--CD--NE2
ATOM CB CT2 -0.18 ! | | | \
ATOM HB1 HA 0.09 ! | HB2 HG2 HE22 (trans to OE1)
ATOM HB2 HA 0.09 ! O=C
GROUP ! |
ATOM CG CT2 -0.18
ATOM HG1 HA 0.09
ATOM HG2 HA 0.09
GROUP
ATOM CD CC 0.55
ATOM OE1 O -0.55
GROUP
ATOM NE2 NH2 -0.62
ATOM HE21 H 0.32
ATOM HE22 H 0.30
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD CG NE2 CD
BOND N HN N CA C CA
BOND C +N CA HA CB HB1 CB HB2 CG HG1
BOND CG HG2 NE2 HE21 NE2 HE22
DOUBLE O C CD OE1
IMPR N -C CA HN C CA +N O
IMPR CD NE2 CG OE1 CD CG NE2 OE1
IMPR NE2 CD HE21 HE22 NE2 CD HE22 HE21
CMAP -C N CA C N CA C +N
DONOR HN N
DONOR HE21 NE2
DONOR HE22 NE2
ACCEPTOR OE1 CD
ACCEPTOR O C
IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984
IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180
IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463
IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291
IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461
IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538
IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832
IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534
IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147
IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140
IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320
IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112
IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094
IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294
IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530
IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959
IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943
RESI GLU -1.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 HG1 OE1
ATOM HA HB 0.09 ! | | | //
GROUP ! HA-CA--CB--CG--CD
ATOM CB CT2 -0.18 ! | | | \
ATOM HB1 HA 0.09 ! | HB2 HG2 OE2(-)
ATOM HB2 HA 0.09 ! O=C
GROUP ! |
ATOM CG CT2 -0.28
ATOM HG1 HA 0.09
ATOM HG2 HA 0.09
ATOM CD CC 0.62
ATOM OE1 OC -0.76
ATOM OE2 OC -0.76
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD CG OE2 CD
BOND N HN N CA C CA
BOND C +N CA HA CB HB1 CB HB2 CG HG1
BOND CG HG2
DOUBLE O C CD OE1
IMPR N -C CA HN C CA +N O
IMPR CD CG OE2 OE1
CMAP -C N CA C N CA C +N
DONOR HN N
ACCEPTOR OE1 CD
ACCEPTOR OE2 CD
ACCEPTOR O C
IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961
IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216
IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501
IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306
IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530
IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516
IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828
IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557
IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145
IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131
IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307
IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053
IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081
IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590
IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532
RESI GLY 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! N-H
ATOM CA CT2 -0.02 ! |
ATOM HA1 HB 0.09 ! |
ATOM HA2 HB 0.09 ! HA1-CA-HA2
GROUP ! |
ATOM C C 0.51 ! |
ATOM O O -0.51 ! C=O
! |
BOND N HN N CA C CA
BOND C +N CA HA1 CA HA2
DOUBLE O C
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
DONOR HN N
ACCEPTOR O C
IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992
IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971
IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479
IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289
IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560
IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814
IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817
PATCHING FIRS GLYP
RESI HSD 0.00 ! neutral HIS, proton on ND1
GROUP
ATOM N NH1 -0.47 ! | HD1 HE1
ATOM HN H 0.31 ! HN-N | /
ATOM CA CT1 0.07 ! | HB1 ND1--CE1
ATOM HA HB 0.09 ! | | / ||
GROUP ! HA-CA--CB--CG ||
ATOM CB CT2 -0.09 ! | | \\ ||
ATOM HB1 HA 0.09 ! | HB2 CD2--NE2
ATOM HB2 HA 0.09 ! O=C |
ATOM ND1 NR1 -0.36 ! | HD2
ATOM HD1 H 0.32
ATOM CG CPH1 -0.05
GROUP
ATOM CE1 CPH2 0.25
ATOM HE1 HR1 0.13
ATOM NE2 NR2 -0.70
ATOM CD2 CPH1 0.22
ATOM HD2 HR3 0.10
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB ND1 CG CE1 ND1
BOND NE2 CD2 N HN N CA
BOND C CA C +N CA HA CB HB1
BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1
DOUBLE O C CG CD2 CE1 NE2
IMPR ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1
IMPR ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
DONOR HN N
DONOR HD1 ND1
ACCEPTOR NE2
ACCEPTOR O C
IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988
IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166
IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509
IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273
IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545
IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519
IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830
IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041
IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118
IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121
IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783
IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597
IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549
IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817
IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932
IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005
IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834
RESI HSE 0.00 ! neutral His, proton on NE2
GROUP
ATOM N NH1 -0.47 ! | HE1
ATOM HN H 0.31 ! HN-N __ /
ATOM CA CT1 0.07 ! | HB1 ND1--CE1
ATOM HA HB 0.09 ! | | / |
GROUP ! HA-CA--CB--CG |
ATOM CB CT2 -0.08 ! | | \\ |
ATOM HB1 HA 0.09 ! | HB2 CD2--NE2
ATOM HB2 HA 0.09 ! O=C | \
ATOM ND1 NR2 -0.70 ! | HD2 HE2
ATOM CG CPH1 0.22
ATOM CE1 CPH2 0.25
ATOM HE1 HR1 0.13
GROUP
ATOM NE2 NR1 -0.36
ATOM HE2 H 0.32
ATOM CD2 CPH1 -0.05
ATOM HD2 HR3 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB ND1 CG
BOND NE2 CD2 N HN N CA
BOND C CA C +N NE2 CE1 CA HA CB HB1
BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1
DOUBLE O C CD2 CG CE1 ND1
IMPR NE2 CD2 CE1 HE2 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1
IMPR NE2 CE1 CD2 HE2 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
DONOR HN N
DONOR HE2 NE2
ACCEPTOR ND1
ACCEPTOR O C
IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991
IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166
IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446
IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290
IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505
IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578
IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833
IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109
IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114
IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101
IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859
IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596
IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170
IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782
IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929
IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996
IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809
RESI HSP 1.00 ! Protonated His
GROUP
ATOM N NH1 -0.47 ! | HD1 HE1
ATOM HN H 0.31 ! HN-N | /
ATOM CA CT1 0.07 ! | HB1 ND1--CE1
ATOM HA HB 0.09 ! | | / ||
GROUP ! HA-CA--CB--CG ||
ATOM CB CT2 -0.05 ! | | \\ ||
ATOM HB1 HA 0.09 ! | HB2 CD2--NE2(+)
ATOM HB2 HA 0.09 ! O=C | \
ATOM CD2 CPH1 0.19 ! | HD2 HE2
ATOM HD2 HR1 0.13
ATOM CG CPH1 0.19
GROUP
ATOM NE2 NR3 -0.51
ATOM HE2 H 0.44
ATOM ND1 NR3 -0.51
ATOM HD1 H 0.44
ATOM CE1 CPH2 0.32
ATOM HE1 HR2 0.18
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB ND1 CG CE1 ND1
BOND NE2 CD2 N HN N CA
BOND C CA C +N CA HA CB HB1
BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1
DOUBLE O C CD2 CG NE2 CE1
IMPR ND1 CG CE1 HD1 ND1 CE1 CG HD1
IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
DONOR HN N
DONOR HD1 ND1
DONOR HE2 NE2
ACCEPTOR O C
IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041
IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225
IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464
IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284
IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521
IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533
IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832
IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168
IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116
IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132
IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718
IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549
IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262
IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727
IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799
IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020
IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018
IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867
RESI ILE 0.00
GROUP
ATOM N NH1 -0.47 ! | HG21 HG22
ATOM HN H 0.31 ! HN-N | /
ATOM CA CT1 0.07 ! | CG2--HG23
ATOM HA HB 0.09 ! | /
GROUP ! HA-CA--CB-HB HD1
ATOM CB CT1 -0.09 ! | \ /
ATOM HB HA 0.09 ! | CG1--CD--HD2
GROUP ! O=C / \ \
ATOM CG2 CT3 -0.27 ! | HG11 HG12 HD3
ATOM HG21 HA 0.09
ATOM HG22 HA 0.09
ATOM HG23 HA 0.09
GROUP
ATOM CG1 CT2 -0.18
ATOM HG11 HA 0.09
ATOM HG12 HA 0.09
GROUP
ATOM CD CT3 -0.27
ATOM HD1 HA 0.09
ATOM HD2 HA 0.09
ATOM HD3 HA 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG1 CB CG2 CB CD CG1
BOND N HN N CA C CA C +N
BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21
BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3
DOUBLE O C
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
DONOR HN N
ACCEPTOR O C
IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978
IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190
IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465
IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300
IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467
IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681
IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826
IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498
IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195
IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452
IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100
IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102
IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105
IC CA CB CG1 CD 1.5681 113.6300 180.0000 114.0900 1.5381
IC CD CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130
IC CD CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141
IC CB CG1 CD HD1 1.5498 114.0900 -176.7800 110.3100 1.1115
IC HD1 CG1 *CD HD2 1.1115 110.3100 119.7500 110.6500 1.1113
IC HD1 CG1 *CD HD3 1.1115 110.3100 -119.7000 111.0200 1.1103
RESI LEU 0.00
GROUP
ATOM N NH1 -0.47 ! | HD11 HD12
ATOM HN H 0.31 ! HN-N | /
ATOM CA CT1 0.07 ! | HB1 CD1--HD13
ATOM HA HB 0.09 ! | | /
GROUP ! HA-CA--CB--CG-HG
ATOM CB CT2 -0.18 ! | | \
ATOM HB1 HA 0.09 ! | HB2 CD2--HD23
ATOM HB2 HA 0.09 ! O=C | \
GROUP ! | HD21 HD22
ATOM CG CT1 -0.09
ATOM HG HA 0.09
GROUP
ATOM CD1 CT3 -0.27
ATOM HD11 HA 0.09
ATOM HD12 HA 0.09
ATOM HD13 HA 0.09
GROUP
ATOM CD2 CT3 -0.27
ATOM HD21 HA 0.09
ATOM HD22 HA 0.09
ATOM HD23 HA 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD1 CG CD2 CG
BOND N HN N CA C CA C +N
BOND CA HA CB HB1 CB HB2 CG HG CD1 HD11
BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23
DOUBLE O C
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
DONOR HN N
ACCEPTOR O C
IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979
IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184
IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463
IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299
IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467
IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543
IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824
IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472
IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145
IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126
IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361
IC CD1 CB *CG CD2 1.5361 110.4800 120.0000 112.5700 1.5360
IC CD1 CD2 *CG HG 1.5361 110.2600 120.0000 108.0200 1.1168
IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111
IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112
IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108
IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116
IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086
IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115
RESI LYS 1.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE1 HZ1
ATOM HA HB 0.09 ! | | | | | /
GROUP ! HA-CA--CB--CG--CD--CE--NZ--HZ2
ATOM CB CT2 -0.18 ! | | | | | \
ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 HE2 HZ3
ATOM HB2 HA 0.09 ! O=C
GROUP ! |
ATOM CG CT2 -0.18
ATOM HG1 HA 0.09
ATOM HG2 HA 0.09
GROUP
ATOM CD CT2 -0.18
ATOM HD1 HA 0.09
ATOM HD2 HA 0.09
GROUP
ATOM CE CT2 0.21
ATOM HE1 HA 0.05
ATOM HE2 HA 0.05
ATOM NZ NH3 -0.30
ATOM HZ1 HC 0.33
ATOM HZ2 HC 0.33
ATOM HZ3 HC 0.33
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD CG CE CD NZ CE
BOND N HN N CA C CA
BOND C +N CA HA CB HB1 CB HB2 CG HG1
BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2
DOUBLE O C
BOND NZ HZ1 NZ HZ2 NZ HZ3
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
DONOR HN N
DONOR HZ1 NZ
DONOR HZ2 NZ
DONOR HZ3 NZ
ACCEPTOR O C
IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988
IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187
IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478
IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277
IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487
IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568
IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833
IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435
IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146
IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131
IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397
IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138
IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143
IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350
IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141
IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146
IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604
IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128
IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123
IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404
IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402
IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401
RESI MET 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 HG1 HE1
ATOM HA HB 0.09 ! | | | |
GROUP ! HA-CA--CB--CG--SD--CE--HE3
ATOM CB CT2 -0.18 ! | | | |
ATOM HB1 HA 0.09 ! | HB2 HG2 HE2
ATOM HB2 HA 0.09 ! O=C
GROUP ! |
ATOM CG CT2 -0.14
ATOM HG1 HA 0.09
ATOM HG2 HA 0.09
ATOM SD S -0.09
ATOM CE CT3 -0.22
ATOM HE1 HA 0.09
ATOM HE2 HA 0.09
ATOM HE3 HA 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB SD CG CE SD
BOND N HN N CA C CA C +N
BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2
BOND CE HE1 CE HE2 CE HE3
DOUBLE O C
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
DONOR HN N
ACCEPTOR O C
IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978
IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195
IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471
IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288
IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471
IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546
IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832
IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460
IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153
IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129
IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219
IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106
IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119
IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206
IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111
IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115
IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112
RESI PHE 0.00
GROUP
ATOM N NH1 -0.47 ! | HD1 HE1
ATOM HN H 0.31 ! HN-N | |
ATOM CA CT1 0.07 ! | HB1 CD1--CE1
ATOM HA HB 0.09 ! | | // \\
GROUP ! HA-CA--CB--CG CZ--HZ
ATOM CB CT2 -0.18 ! | | \ __ /
ATOM HB1 HA 0.09 ! | HB2 CD2--CE2
ATOM HB2 HA 0.09 ! O=C | |
GROUP ! | HD2 HE2
ATOM CG CA 0.00
GROUP
ATOM CD1 CA -0.115
ATOM HD1 HP 0.115
GROUP
ATOM CE1 CA -0.115
ATOM HE1 HP 0.115
GROUP
ATOM CZ CA -0.115
ATOM HZ HP 0.115
GROUP
ATOM CD2 CA -0.115
ATOM HD2 HP 0.115
GROUP
ATOM CE2 CA -0.115
ATOM HE2 HP 0.115
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD2 CG CE1 CD1
BOND CZ CE2 N HN
BOND N CA C CA C +N CA HA
BOND CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1
DOUBLE O C CD1 CG CZ CE1 CE2 CD2
BOND CE2 HE2 CZ HZ
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
DONOR HN N
ACCEPTOR O C
IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987
IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229
IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483
IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287
IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523
IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594
IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832
IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109
IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119
IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113
IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059
IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062
IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006
IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814
IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002
IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811
IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004
IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808
IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811
IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807
RESI PRO 0.00
GROUP ! HD1 HD2
ATOM N N -0.29 ! | \ /
ATOM CD CP3 0.00 ! N---CD HG1 ATOM CA CP1 0.02
ATOM HD1 HA 0.09 ! | \ /
ATOM HD2 HA 0.09 ! | CG
ATOM CA CP1 0.02 ! | / \
ATOM HA HB 0.09 ! HA-CA--CB HG2
GROUP ! | / \
ATOM CB CP2 -0.18 ! | HB1 HB2
ATOM HB1 HA 0.09 ! O=C
ATOM HB2 HA 0.09 ! |
GROUP
ATOM CG CP2 -0.18
ATOM HG1 HA 0.09
ATOM HG2 HA 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND C CA C +N
BOND N CA CA CB CB CG CG CD N CD
BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB
DOUBLE O C
IMPR N -C CA CD
IMPR C CA +N O
CMAP -C N CA C N CA C +N
ACCEPTOR O C
IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624
IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399
IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569
IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316
IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517
IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399
IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837
IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322
IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317
IC N CA CB HB1 1.4585 102.5600 -84.9400 109.0200 1.1131
IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088
IC CA CB CG HG1 1.5399 104.3900 -156.7200 112.9500 1.1077
IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143
IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137
IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144
PATCHING FIRS PROP
RESI SER 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1
ATOM HA HB 0.09 ! | |
GROUP ! HA-CA--CB--OG
ATOM CB CT2 0.05 ! | | \
ATOM HB1 HA 0.09 ! | HB2 HG1
ATOM HB2 HA 0.09 ! O=C
ATOM OG OH1 -0.66 ! |
ATOM HG1 H 0.43
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA OG CB N HN N CA
BOND C CA C +N CA HA CB HB1
BOND CB HB2 OG HG1
DOUBLE O C
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
DONOR HN N
DONOR HG1 OG
ACCEPTOR OG
ACCEPTOR O C
IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999
IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166
IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448
IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290
IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529
IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585
IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821
IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341
IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140
IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136
IC CA CB OG HG1 1.5585 112.4500 165.9600 107.0800 0.9655
RESI THR 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | OG1--HG1
ATOM HA HB 0.09 ! | /
GROUP ! HA-CA--CB-HB
ATOM CB CT1 0.14 ! | \
ATOM HB HA 0.09 ! | CG2--HG21
ATOM OG1 OH1 -0.66 ! O=C / \
ATOM HG1 H 0.43 ! | HG21 HG22
GROUP
ATOM CG2 CT3 -0.27
ATOM HG21 HA 0.09
ATOM HG22 HA 0.09
ATOM HG23 HA 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA OG1 CB CG2 CB N HN
BOND N CA C CA C +N CA HA
BOND CB HB OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23
DOUBLE O C
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
DONOR HN N
DONOR HG1 OG1
ACCEPTOR OG1
ACCEPTOR O C
IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995
IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162
IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449
IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294
IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525
IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693
IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817
IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252
IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174
IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324
IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633
IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104
IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109
IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113
RESI TRP 0.00
GROUP
ATOM N NH1 -0.47 ! | HE3
ATOM HN H 0.31 ! HN-N |
ATOM CA CT1 0.07 ! | HB1 CE3
ATOM HA HB 0.09 ! | | / \\
GROUP ! HA-CA--CB---CG-----CD2 CZ3-HZ3
ATOM CB CT2 -0.18 ! | | || || |
ATOM HB1 HA 0.09 ! | HB2 CD1 CE2 CH2-HH2
ATOM HB2 HA 0.09 ! O=C / \ / \ //
GROUP ! | HD1 NE1 CZ2
ATOM CG CY -0.03 ! | |
ATOM CD1 CA 0.035 ! HE1 HZ2
ATOM HD1 HP 0.115
ATOM NE1 NY -0.61
ATOM HE1 H 0.38
ATOM CE2 CPT 0.13
ATOM CD2 CPT -0.02
GROUP
ATOM CE3 CA -0.115
ATOM HE3 HP 0.115
GROUP
ATOM CZ3 CA -0.115
ATOM HZ3 HP 0.115
GROUP
ATOM CZ2 CA -0.115
ATOM HZ2 HP 0.115
GROUP
ATOM CH2 CA -0.115
ATOM HH2 HP 0.115
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD2 CG NE1 CD1
BOND CZ2 CE2
BOND N HN N CA C CA C +N
BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1
BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2
BOND CZ3 HZ3 CH2 HH2
DOUBLE O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
DONOR HN N
DONOR HE1 NE1
ACCEPTOR O C
IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972
IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202
IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505
IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304
IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526
IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560
IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835
IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233
IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127
IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118
IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407
IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679
IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126
IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746
IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011
IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017
IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019
IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030
IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815
IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811
IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811
IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790
IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767
IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820
RESI TYR 0.00
GROUP
ATOM N NH1 -0.47 ! | HD1 HE1
ATOM HN H 0.31 ! HN-N | |
ATOM CA CT1 0.07 ! | HB1 CD1--CE1
ATOM HA HB 0.09 ! | | // \\
GROUP ! HA-CA--CB--CG CZ--OH
ATOM CB CT2 -0.18 ! | | \ __ / \
ATOM HB1 HA 0.09 ! | HB2 CD2--CE2 HH
ATOM HB2 HA 0.09 ! O=C | |
GROUP ! | HD2 HE2
ATOM CG CA 0.00
GROUP
ATOM CD1 CA -0.115
ATOM HD1 HP 0.115
GROUP
ATOM CE1 CA -0.115
ATOM HE1 HP 0.115
GROUP
ATOM CZ CA 0.11
ATOM OH OH1 -0.54
ATOM HH H 0.43
GROUP
ATOM CD2 CA -0.115
ATOM HD2 HP 0.115
GROUP
ATOM CE2 CA -0.115
ATOM HE2 HP 0.115
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD2 CG CE1 CD1
BOND CZ CE2 OH CZ
BOND N HN N CA C CA C +N
BOND CA HA CB HB1 CB HB2 CD1 HD1 CD2 HD2
BOND CE1 HE1 CE2 HE2 OH HH
DOUBLE O C CD1 CG CE1 CZ CE2 CD2
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
DONOR HN N
DONOR HH OH
ACCEPTOR OH
ACCEPTOR O C
IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986
IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232
IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484
IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287
IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513
IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606
IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833
IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113
IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119
IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115
IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064
IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068
IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026
IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814
IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022
IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813
IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978
IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799
IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798
IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063
IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594
RESI VAL 0.00
GROUP
ATOM N NH1 -0.47 ! | HG11 HG12
ATOM HN H 0.31 ! HN-N | /
ATOM CA CT1 0.07 ! | CG1--HG13
ATOM HA HB 0.09 ! | /
GROUP ! HA-CA--CB-HB
ATOM CB CT1 -0.09 ! | \
ATOM HB HA 0.09 ! | CG2--HG21
GROUP ! O=C / \
ATOM CG1 CT3 -0.27 ! | HG21 HG22
ATOM HG11 HA 0.09
ATOM HG12 HA 0.09
ATOM HG13 HA 0.09
GROUP
ATOM CG2 CT3 -0.27
ATOM HG21 HA 0.09
ATOM HG22 HA 0.09
ATOM HG23 HA 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG1 CB CG2 CB N HN
BOND N CA C CA C +N CA HA
BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21
BOND CG2 HG22 CG2 HG23
DOUBLE O C
IMPR N -C CA HN C CA +N O
CMAP -C N CA C N CA C +N
DONOR HN N
ACCEPTOR O C
IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966
IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180
IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471
IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297
IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471
IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660
IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828
IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441
IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414
IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178
IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114
IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097
IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110
IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108
IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115
IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098
RESI ALAD 0.00 ! Alanine dipeptide, with CMAP term
GROUP
ATOM CL CT3 -0.27
ATOM HL1 HA 0.09
ATOM HL2 HA 0.09
ATOM HL3 HA 0.09
GROUP
ATOM CLP C 0.51
ATOM OL O -0.51
GROUP
ATOM NL NH1 -0.47
ATOM HL H 0.31
ATOM CA CT1 0.07
ATOM HA HB 0.09
GROUP
ATOM CB CT3 -0.27 ! HL1 OL OR HR1
ATOM HB1 HA 0.09 ! \ || HL HA || HR /
ATOM HB2 HA 0.09 ! \ || | | || | /
ATOM HB3 HA 0.09 ! HL2---CL--CLP--NL--CA--CRP--NR---CR---HR2
GROUP ! / | \
ATOM CRP C 0.51 ! / HB1--CB--HB3 \
ATOM OR O -0.51 ! HL3 | HR3
GROUP ! HB2
ATOM NR NH1 -0.47
ATOM HR H 0.31
ATOM CR CT3 -0.11
ATOM HR1 HA 0.09
ATOM HR2 HA 0.09
ATOM HR3 HA 0.09
BOND CL CLP CLP NL NL CA
BOND CA CRP CRP NR NR CR
DOUBLE CLP OL CRP OR
BOND NL HL NR HR
BOND CA HA CA CB
BOND CL HL1 CL HL2 CL HL3
BOND CB HB1 CB HB2 CB HB3
BOND CR HR1 CR HR2 CR HR3
IMPR CLP CL NL OL NL CLP CA HL
IMPR CRP CA NR OR NR CRP CR HR
CMAP CLP NL CA CRP NL CA CRP NR
ic clp nl ca crp 0.0 0.0 180.0 0.0 0.0 ! Phi
ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0
ic hl nl ca crp 0.0 0.0 0.0 0.0 0.0
ic nl ca crp nr 0.0 0.0 180.0 0.0 0.0 ! Psi
ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0
ic nl ca crp or 0.0 0.0 0.0 0.0 0.0
ic cl clp nl ca 0.0 0.0 180.0 0.0 0.0 ! Omega Left
ic nl cl *clp ol 0.0 0.0 180.0 0.0 0.0
ic ol clp nl ca 0.0 0.0 0.0 0.0 0.0
ic ca crp nr cr 0.0 0.0 180.0 0.0 0.0 ! Omega Right
ic crp cr *nr hr 0.0 0.0 180.0 0.0 0.0
ic ca crp nr hr 0.0 0.0 180.0 0.0 0.0
ic nl crp *ca ha 0.0 0.0 240.0 0.0 0.0
ic nl crp *ca cb 0.0 0.0 120.0 0.0 0.0
ic hl1 cl clp nl 0.0 0.0 180.0 0.0 0.0
ic hl2 cl clp nl 0.0 0.0 60.0 0.0 0.0
ic hl3 cl clp ol 0.0 0.0 120.0 0.0 0.0
ic ha ca cb hb1 0.0 0.0 180.0 0.0 0.0
ic nl ca cb hb2 0.0 0.0 180.0 0.0 0.0
ic crp ca cb hb3 0.0 0.0 180.0 0.0 0.0
ic crp nr cr hr1 0.0 0.0 180.0 0.0 0.0
ic crp nr cr hr2 0.0 0.0 60.0 0.0 0.0
ic hr nr cr hr3 0.0 0.0 120.0 0.0 0.0
ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0
ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0
ic hb1 hb2 *cb hb3 0.0 0.0 120.0 0.0 0.0
ic hl1 hl2 *cl hl3 0.0 0.0 240.0 0.0 0.0
ic hr1 hr2 *cr hr3 0.0 0.0 240.0 0.0 0.0
ic ha ca nl hl 0.0 0.0 240.0 0.0 0.0
patch first none last none
RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral
GROUP
ATOM OH2 OT -0.834
ATOM H1 HT 0.417
ATOM H2 HT 0.417
BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake
ANGLE H1 OH2 H2 ! required
ACCEPTOR OH2
PATCHING FIRS NONE LAST NONE
RESI TP3M 0.000 ! "mmff" water model, as an analog of tip3p
GROUP
ATOM OH2 OT -0.834 ! these charges are replaced by the mmff setup
ATOM H1 HT 0.417 ! these charges are replaced by the mmff setup
ATOM H2 HT 0.417 ! these charges are replaced by the mmff setup
BOND OH2 H1 OH2 H2 ! omits the H1-H2 bond, which is needed for shake with tip3p
ANGLE H1 OH2 H2 ! required
ACCEPTOR OH2
PATCHING FIRS NONE LAST NONE
! Ion parameters from Benoit Roux and Coworkers
! As of 8/98 no NBFIX terms required
!
RESI SOD 1.00 ! Sodium Ion
GROUP
ATOM SOD SOD 1.00
PATCHING FIRST NONE LAST NONE
RESI MG 2.00 ! Magnesium Ion
GROUP
ATOM MG MG 2.00
PATCHING FIRST NONE LAST NONE
RESI POT 1.00 ! Potassium Ion
GROUP
ATOM POT POT 1.00
PATCHING FIRST NONE LAST NONE
RESI CES 1.00 ! Cesium Ion
GROUP
ATOM CES CES 1.00
PATCHING FIRST NONE LAST NONE
RESI CAL 2.00 ! Calcium Ion
GROUP
ATOM CAL CAL 2.00
PATCHING FIRST NONE LAST NONE
RESI CLA -1.00 ! Chloride Ion
GROUP
ATOM CLA CLA -1.00
PATCHING FIRST NONE LAST NONE
RESI ZN2 2.00 ! Zinc ion, Roland Stote
GROUP
ATOM ZN ZN 2.00
PATCHING FIRST NONE LAST NONE
PRES NTER 1.00 ! standard N-terminus
GROUP ! use in generate statement
ATOM N NH3 -0.30 !
ATOM HT1 HC 0.33 ! HT1
ATOM HT2 HC 0.33 ! (+)/
ATOM HT3 HC 0.33 ! --CA--N--HT2
ATOM CA CT1 0.21 ! | \
ATOM HA HB 0.10 ! HA HT3
DELETE ATOM HN
BOND HT1 N HT2 N HT3 N
DONOR HT1 N
DONOR HT2 N
DONOR HT3 N
IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000
IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000
IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000
PRES GLYP 1.00 ! Glycine N-terminus
GROUP ! use in generate statement
ATOM N NH3 -0.30 !
ATOM HT1 HC 0.33 ! HA1 HT1
ATOM HT2 HC 0.33 ! | (+)/
ATOM HT3 HC 0.33 ! --CA--N--HT2
ATOM CA CT2 0.13 ! | \
ATOM HA1 HB 0.09 ! HA2 HT3
ATOM HA2 HB 0.09 !
DELETE ATOM HN
BOND HT1 N HT2 N HT3 N
DONOR HT1 N
DONOR HT2 N
DONOR HT3 N
IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000
IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000
IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000
PRES PROP 1.00 ! Proline N-Terminal
GROUP ! use in generate statement
ATOM N NP -0.07 ! HA
ATOM HN1 HC 0.24 ! |
ATOM HN2 HC 0.24 ! -CA HN1
ATOM CD CP3 0.16 ! / \ /
ATOM HD1 HA 0.09 ! N(+)
ATOM HD2 HA 0.09 ! / \
ATOM CA CP1 0.16 ! -CD HN2
ATOM HA HB 0.09 ! | \
BOND HN1 N HN2 N ! HD1 HD2
DONOR HN1 N
DONOR HN2 N
IC HN1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000
IC HN2 CA *N HN1 0.0000 0.0000 120.0000 0.0000 0.0000
PRES ACE 0.00 ! acetylated N-terminus
! do NOT use to create dipeptides, see ACED
GROUP ! use in generate statement
ATOM CAY CT3 -0.27 !
ATOM HY1 HA 0.09 ! HY1 HY2 HY3
ATOM HY2 HA 0.09 ! \ | /
ATOM HY3 HA 0.09 ! CAY
GROUP ! |
ATOM CY C 0.51 ! CY=OY
ATOM OY O -0.51 ! |
!
BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3
DOUBLE OY CY
IMPR CY CAY N OY
IMPR N CY CA HN
CMAP CY N CA C N CA C +N
ACCEPTOR OY CY
IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000
IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000
IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000
IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000
IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000
IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000
IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000
PRES ACED 0.00 ! acetylated N-terminus (to create dipeptide)
GROUP ! use in generate statement
ATOM CAY CT3 -0.27 !
ATOM HY1 HA 0.09 ! HY1 HY2 HY3
ATOM HY2 HA 0.09 ! \ | /
ATOM HY3 HA 0.09 ! CAY
GROUP ! |
ATOM CY C 0.51 ! CY=OY
ATOM OY O -0.51 ! |
!
BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3
DOUBLE OY CY
IMPR CY CAY N OY
IMPR N CY CA HN
CMAP CY N CA C N CA C NT
ACCEPTOR OY CY
IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000
IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000
IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000
IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000
IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000
IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000
IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000
PRES ACP 0.00 ! acetylated N-terminus
! NOT for proline dipeptide, see ACPD
GROUP ! use in generate statement
ATOM CAY CT3 -0.27 !
ATOM HY1 HA 0.09 ! HY1 HY2 HY3
ATOM HY2 HA 0.09 ! \ | /
ATOM HY3 HA 0.09 ! CAY
GROUP ! |
ATOM CY C 0.51 ! CY=OY
ATOM OY O -0.51 ! |
!
BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3
DOUBLE OY CY
IMPR CY CAY N OY
IMPR N CY CA CD
CMAP CY N CA C N CA C +N
ACCEPTOR OY CY
IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000
IC CY CA *N CD 0.0000 0.0000 180.0000 0.0000 0.0000
IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000
IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000
IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000
IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000
IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000
PRES ACPD 0.00 ! acetylated N-terminus (for proline dipeptide)
GROUP ! use in generate statement
ATOM CAY CT3 -0.27 !
ATOM HY1 HA 0.09 ! HY1 HY2 HY3
ATOM HY2 HA 0.09 ! \ | /
ATOM HY3 HA 0.09 ! CAY
GROUP ! |
ATOM CY C 0.51 ! CY=OY
ATOM OY O -0.51 ! |
!
BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3
DOUBLE OY CY
IMPR CY CAY N OY
IMPR N CY CA CD
CMAP CY N CA C N CA C NT
ACCEPTOR OY CY
IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000
IC CY CA *N CD 0.0000 0.0000 180.0000 0.0000 0.0000
IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000
IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000
IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000
IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000
IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000
PRES NNEU 0.00 ! neutral N-terminus; charges from LSN
GROUP ! use in generate statement
ATOM N NH2 -0.96 !
ATOM HT1 H 0.34 ! HT1
ATOM HT2 H 0.34 ! /
! --CA--N--HT2
ATOM CA CT1 0.19 ! | ! change to CT2 for neutral N terminal glycine
ATOM HA HB 0.09 ! HA ! change to HA1 and HB2 and add HA2 atom for N terminal glycine
DELETE ATOM HN
BOND HT1 N HT2 N
DONOR HT1 N
DONOR HT2 N
IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000
IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000
PRES CTER -1.00 ! standard C-terminus
GROUP ! use in generate statement
ATOM C CC 0.34 ! OT2(-)
ATOM OT1 OC -0.67 ! /
ATOM OT2 OC -0.67 ! -C
DELETE ATOM O ! \\
BOND C OT2 ! OT1
DOUBLE C OT1
IMPR C CA OT2 OT1
ACCEPTOR OT1 C
ACCEPTOR OT2 C
IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000
IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
PRES CT1 0.00 ! methylated C-terminus from methyl acetate
GROUP ! use in generate statement
ATOM N NH1 -0.47 !
ATOM HN H 0.31 ! OT1
ATOM CA CT1 0.17 ! | //
ATOM HA HB 0.09 ! -N--CA--C HT1
ATOM C CD 0.63 ! | | \ /
ATOM OT1 OB -0.52 ! HN HA OT2--CT--HT2
ATOM OT2 OS -0.34 ! \
ATOM CT CT3 -0.14 ! HT3
ATOM HT1 HA 0.09 !
ATOM HT2 HA 0.09 !
ATOM HT3 HA 0.09 !
DELETE ATOM O
BOND C OT2 OT2 CT
BOND CT HT1 CT HT2 CT HT3
DOUBLE C OT1
IMPR C CA OT2 OT1
ACCEPTOR OT1 C
ACCEPTOR OT2 C
IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000
IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000
IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000
IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000
IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000
PRES CT2 0.00 ! amidated C-terminus
GROUP ! use in generate statement
ATOM C CC 0.55 !
ATOM O O -0.55 ! |
GROUP ! O=C
ATOM NT NH2 -0.62 ! |
ATOM HT1 H 0.32 ! NT
ATOM HT2 H 0.30 ! / \
BOND C NT ! HT1 HT2 (HT1 is cis to O)
BOND NT HT1 NT HT2 !
IMPR C NT CA O C CA NT O
IMPR NT C HT1 HT2 NT C HT2 HT1
DONOR HT1 NT
DONOR HT2 NT
IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000
IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000
IC CA C NT HT1 0.0000 0.0000 180.0000 0.0000 0.0000
IC HT1 C *NT HT2 0.0000 0.0000 180.0000 0.0000 0.0000
PRES CT3 0.00 ! N-Methylamide C-terminus
GROUP ! use in generate statement
ATOM C C 0.51 !
ATOM O O -0.51 ! |
GROUP ! C=O
ATOM NT NH1 -0.47 ! |
ATOM HNT H 0.31 ! NT-HNT
ATOM CAT CT3 -0.11 ! |
ATOM HT1 HA 0.09 ! HT1-CAT-HT3
ATOM HT2 HA 0.09 ! |
ATOM HT3 HA 0.09 ! HT2
!
BOND C NT NT HNT NT CAT CAT HT1 CAT HT2 CAT HT3
IMPR NT C CAT HNT C CA NT O
CMAP -C N CA C N CA C NT
DONOR HNT NT
IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000
IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000
IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000
IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000
IC C NT CAT HT1 0.0000 0.0000 60.0000 0.0000 0.0000
IC C NT CAT HT2 0.0000 0.0000 180.0000 0.0000 0.0000
IC C NT CAT HT3 0.0000 0.0000 -60.0000 0.0000 0.0000
PRES CNEU 0.00 ! neutral C-terminus; charges from ASPP
GROUP ! use in generate statement; C reduced to balance
ATOM C CD 0.72 ! OT2-HT2
ATOM OT1 OB -0.55 ! /
ATOM OT2 OH1 -0.61 ! -C
ATOM HT2 H 0.44 ! \\
DELETE ATOM O ! OT1
BOND C OT2 !
BOND OT2 HT2
DOUBLE C OT1
IMPR C CA OT2 OT1
ACCEPTOR OT1 C
ACCEPTOR OT2 C
IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000
IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
IC CA C OT2 HT2 0.0000 0.0000 180.0000 0.0000 0.0000
PRES ASPP 0.00 ! patch for protonated aspartic acid, proton on od2
GROUP ! via acetic acid, use in a patch statementand
! follow with AUTOgenerate ANGLes DIHEdrals command
ATOM CB CT2 -0.21 !
ATOM HB1 HA 0.09 ! HB1 OD1
ATOM HB2 HA 0.09 ! | //
ATOM CG CD 0.75 ! -CB--CG
ATOM OD1 OB -0.55 ! | \
ATOM OD2 OH1 -0.61 ! HB2 OD2-HD2
ATOM HD2 H 0.44 !
BOND OD2 HD2
DONOR HD2 OD2
IC HD2 OD2 CG OD1 0.0000 0.0000 0.0000 0.0000 0.0000
PRES GLUP 0.00 ! patch for protonated glutamic acid, proton on oe2
GROUP ! via acetic acid, use in a patch statement and
! follow with AUTOgenerate ANGLes DIHEdrals command
ATOM CG CT2 -0.21 !
ATOM HG1 HA 0.09 ! HG1 OE1
ATOM HG2 HA 0.09 ! | //
ATOM CD CD 0.75 ! -CG--CD
ATOM OE1 OB -0.55 ! | \
ATOM OE2 OH1 -0.61 ! HG2 OE2-HE2
ATOM HE2 H 0.44 !
BOND OE2 HE2
DONOR HE2 OE2
IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000
PRES LSN 0.00 ! patch for neutral lysine based on methylamine
! use in a patch statement
! follow with AUTOgenerate ANGLes DIHEdrals command
!delete atom and reassign charges
DELETE ATOM HZ3
GROUP
ATOM CE CT2 0.13
ATOM HE1 HA 0.075
ATOM HE2 HA 0.075
ATOM NZ NH2 -0.96
ATOM HZ1 HC 0.34
ATOM HZ2 HC 0.34
PRES LINK 0.00 ! linkage for IMAGES or for joining segments
! 1 refers to previous (N terminal)
! 2 refers to next (C terminal)
! use in a patch statement
! follow with AUTOgenerate ANGLes DIHEdrals command
BOND 1C 2N
!the need for the explicit specification of angles and dihedrals in
!patches linking images has not been tested
!ANGLE 1C 2N 2CA 1CA 1C 2N
!ANGLE 1O 1C 2N 1C 2N 2HN
!DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB
!DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N
!DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA
!DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA
IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000
IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000
PRES DISU -0.36 ! patch for disulfides. Patch must be 1-CYS and 2-CYS.
! use in a patch statement
! follow with AUTOgenerate ANGLes DIHEdrals command
GROUP
ATOM 1CB CT2 -0.10 !
ATOM 1SG SM -0.08 ! 2SG--2CB--
GROUP ! /
ATOM 2SG SM -0.08 ! -1CB--1SG
ATOM 2CB CT2 -0.10 !
DELETE ATOM 1HG1
DELETE ATOM 2HG1
BOND 1SG 2SG
IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000
IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
PRES HS2 0.00 ! Patch for neutral His, move proton from ND1 to NE2
! use in a patch statement
! follow with AUTOgenerate ANGLes DIHEdrals command
GROUP
ATOM CE1 CPH2 0.25 ! HE1
ATOM HE1 HR1 0.13 ! /
ATOM ND1 NR2 -0.70 ! HB1 ND1--CE1
ATOM CG CPH1 0.22 ! | / |
ATOM CB CT2 -0.08 ! -CB--CG |
ATOM HB1 HA 0.09 ! | \ |
ATOM HB2 HA 0.09 ! HB2 CD2--NE2
GROUP ! | \
ATOM NE2 NR1 -0.36 ! HD2 HE2
ATOM HE2 H 0.32
ATOM CD2 CPH1 -0.05
ATOM HD2 HR3 0.09
DELETE ATOM HD1
DELETE ACCE NE2
BOND NE2 HE2
IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2
DONOR HE2 NE2
ACCEPTOR ND1
IC CE1 CD2 *NE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000
! patches for cyclic peptides
PRES LIG1 0.00000 ! linkage for cyclic peptide
! 1 refers to the C terminus which is a glycine
! 2 refers to the N terminus
! use in a patch statement, perform initial
! generation using first NONE last NONE
! follow with AUTOgenerate ANGLes DIHEdrals command
BOND 1C 2N
IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000
IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000
PRES LIG2 0.00000 ! linkage for cyclic peptide
! 1 refers to the C terminus
! 2 refers to the N terminus which is a glycine
! use in a patch statement, perform initial
! generation using first NONE last NONE
! follow with AUTOgenerate ANGLes DIHEdrals command
BOND 1C 2N
IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000
IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000
PRES LIG3 0.00000 ! linkage for cyclic peptide
! 1 refers to the C terminus which is a glycine
! 2 refers to the N terminus which is a glycine
! use in a patch statement, perform initial
! generation using first NONE last NONE
! follow with AUTOgenerate ANGLes DIHEdrals command
BOND 1C 2N
IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000
IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000
END
examples/simulateCharmm.py
View file @ cc97a0ba
......@@ -3,31 +3,21 @@ from simtk.openmm import *
from simtk.unit import *
from sys import stdout, exit, stderr
# Define a user-interface
from optparse import OptionParser
parser = OptionParser()
parser.add_option('-t', '--top', dest='top', default=None,
help='CHARMM RTF file to use in the simulation.')
parser.add_option('-p', '--param', dest='par', default=None,
help='CHARMM parameter file to use in the simulation.')
opt, arg = parser.parse_args()
if arg:
stderr.write('Unexpected arguments: %s' % ', '.join(arg) + '\n')
exit(parser.print_help() or 1)
if opt.top is None or opt.par is None:
stderr.write('You must provide a top AND parameter file\n')
exit(parser.print_help() or 1)
# Read the PSF
psf = CharmmPsfFile('ala_ala_ala.psf')
# Get the coordinates from the PDB
pdb = PDBFile('ala_ala_ala.pdb')
# Read and condense the parameter set
params = CharmmParameterSet(opt.top, opt.par)
# Load the parameter set.
params = CharmmParameterSet('charmm22.rtf', 'charmm22.par')
# NOTICE:
# -------
# The CHARMM 22 parameter set is out-of-date and NOT recommended for general
# use. It is included here as an illustrative example, but for production
# simulations you should download the latest versions of the force fields at
# http://mackerell.umaryland.edu/CHARMM_ff_params.html
# Instantiate the system
system = psf.createSystem(params, nonbondedMethod=NoCutoff,
......
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