*>>>>>> Combined CHARMM All-Hydrogen Parameter File for <<<<<<<<<
*>>>>>>> CHARMM22 Proteins and CHARMM27 Nucleic Acids <<<<<<<<<<
*from
*>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<
*>>>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<
*>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
*>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu  <<<<<<<<<
*and
*  \\\\ CHARMM27 All-Hydrogen Nucleic Acid Parameter File ////
*  \\\\\\\\\\\\\\\\\\ Developmental ////////////////////////
*       Alexander D. MacKerell Jr. and Nicolas Foloppe
*                       August 1999
*    All comments to ADM jr.  email: alex,mmiris.ab.umd.edu
*            telephone: 410-706-7442
*

! references
!
!PROTEINS
!
!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.;
!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.;
!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos,
!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III,
!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.;
!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M.  All-atom
!empirical potential for molecular modeling and dynamics Studies of
!proteins.  Journal of Physical Chemistry B, 1998, 102, 3586-3616.
!
!PHOSPHOTYROSINE
!
!Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D. and Lim, C.
!Structural Characterization of the Phosphotyrosine Binding Region of a
!High-Affinity aSH2 Domain-Phosphopeptide Complex by Molecular Dynamics
!Simulation and Chemical Shift Calculations. Journal of the American
!Chemical Society, 1996, 118: 11265-11277.
!
!IONS (see lipid and nucleic acid topology and parameter files for
!additional ions
!
!ZINC
!
!Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and
!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS:
!Structure, Function, and Genetics 23:12-31 (1995)
!
!NUCLEIC ACIDS
!
!Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for
!Nucleic Acids: 2) Parameter Optimization Based on Small Molecule and
!Condensed Phase Macromolecular Target Data.  Journal of Computational
!Chemistry, 2000, 21:86-104.
!
!and
!
!MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for
!Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA
!and RNA in Solution. Journal of Computational
!Chemistry, 2000, 21:105-120.
!
!NAD(P)+, NAD(P)H and PPI
!
!Pavelites, J.J., Bash, P.A., Gao, J. and MacKerell, Jr., A.D. A
!Molecular Mechanics Force Field for NAD+, NADH, and the Pyrophosphate
!Groups of Nucleotides, Journal of Computational Chemistry, 1997, 18:
!221-239.
!
!IONS
!
!all ions from Roux and coworkers
!
!Sodium
!
!Beglov, D. and Roux, B., Finite Representation of an Infinite
!Bulk System: Solvent Boundary Potential for Computer Simulations,
!Journal of Chemical Physics, 1994, 100: 9050-9063
!


BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb          b0
!
! from lipids

! from CHARMm23 guessed parameters
! Rommie Jerome
CC   CPH1 252.000 1.483
CPH1 NC2 360.833 1.412
CN7  CTL3 262.625 1.506
CT2  CTL3 230.594 1.519  
C    HC 330.000 1.100

!lipids section
CTL3  CL    200.0       1.522   ! methyl acetate
CTL2  CL    200.0       1.522   ! methyl acetate
CTL1  CL    200.0       1.522   ! methyl acetate
OBL   CL    750.0       1.220   ! methyl acetate
OCL   CL    525.0       1.260   ! acetate, protein
OSL   CL    150.0       1.334   ! methyl acetate
OHL   CL    230.0       1.40    ! methyl acetate
HOL   OHL   545.0       0.960   ! acetic acid
CTL1  HAL1  309.00      1.111   ! alkanes, 3/92
CTL2  HAL2  309.00      1.111   ! alkanes, 4/98
CTL3  HAL3  322.00      1.111   ! alkanes, 4/98
CTL3  OSL   340.0       1.43    ! phosphate
CTL2  OSL   340.0       1.43    ! phosphate
CTL1  OSL   340.0       1.43    ! phosphate
OSL   PL    270.0       1.60    ! phosphate
O2L   PL    580.0       1.48    ! phosphate
OHL   PL    237.0       1.59    ! phosphate
NH3L  HCL   410.0       1.04    ! ethanolamine
NH3L  CTL2  261.0       1.51    ! ethanolamine
NTL   CTL2  215.00      1.51    ! tetramethylammonium
NTL   CTL5  215.00      1.51    ! tetramethylammonium
CTL5  HL    300.00      1.08    ! tetramethylammonium
CTL2  HL    300.00      1.08    ! tetramethylammonium
CTL1  CTL1  222.500     1.500   ! alkanes, 3/92
CTL1  CTL2  222.500     1.538   ! alkanes, 3/92
CTL1  CTL3  222.500     1.538   ! alkanes, 3/92
CTL2  CTL2  222.500     1.530   ! alkanes, 3/92
CTL2  CTL3  222.500     1.528   ! alkanes, 3/92
CTL3  CTL3  222.500     1.530   ! alkanes, 3/92
OHL   CTL1  428.0       1.420   !  glycerol
OHL   CTL2  428.0       1.420   !  glycerol
OHL   CTL3  428.0       1.420   !  glycerol
SL    O2L   540.0       1.448   ! methylsulfate
SL    OSL   250.0       1.575   ! methylsulfate
!HT    HT      0.0       1.5139  ! from TIPS3P geometry (for SHAKE w/PARAM)
!HT    OT    450.0       0.9572  ! from TIPS3P geometry
CEL2  CEL2  510.000     1.330   ! ethene yin,adm jr., 12/95
HEL2  CEL2  365.000     1.100   ! propene; from ethene, yin,adm jr., 12/95
CEL1  CTL3  383.000     1.504   ! butene, yin,adm jr., 12/95
CEL1  CEL2  500.000     1.342   ! propene, yin,adm jr., 12/95
HEL1  CEL1  360.500     1.100   ! propene, yin,adm jr., 12/95
CEL1  CTL2  365.000     1.502   ! butene; from propene, yin,adm jr., 12/95
CEL1  CEL1  440.000     1.340   ! butene, yin,adm jr., 12/95

!
C    C     600.000     1.3350 ! ALLOW ARO HEM
                ! Heme vinyl substituent (KK, from propene (JCS))
CA   CA    305.000     1.3750 ! ALLOW   ARO
                ! benzene, JES 8/25/89
CE1  CE1   440.000     1.3400   ! 
		! for butene; from propene, yin/adm jr., 12/95
CE1  CE2   500.000     1.3420   ! 
		! for propene, yin/adm jr., 12/95
CE1  CT2   365.000     1.5020   ! 
		! for butene; from propene, yin/adm jr., 12/95
CE1  CT3   383.000     1.5040   ! 
		! for butene, yin/adm jr., 12/95
CE2  CE2   510.000     1.3300   ! 
		! for ethene, yin/adm jr., 12/95
CP1  C     250.000     1.4900 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP1  CC    250.000     1.4900 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP1  CD    200.000     1.4900 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2  CP1   222.500     1.5270 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2  CP2   222.500     1.5370 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3  CP2   222.500     1.5370 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CPB  C     450.000     1.3800 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CPB  CPA   299.800     1.4432 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB  CPB   340.700     1.3464 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPH1 CPH1  410.000     1.3600 ! ALLOW ARO
                ! histidine, adm jr., 6/27/90
CPM  CPA   360.000     1.3716 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPT  CA    305.000     1.3680 ! ALLOW   ARO
                ! adm jr., 12/30/91, for jwk
CPT  CPT   360.000     1.4000 ! ALLOW   ARO
                !adm jr., 12/30/91, for jwk
CT1  C     250.000     1.4900 ! ALLOW   ALI PEP POL ARO
                ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT1  CC    200.000     1.5220 ! ALLOW   POL
                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1  CD    200.000     1.5220 ! ALLOW   POL
                ! adm jr. 5/02/91, acetic acid pure solvent
CT1  CT1   222.500     1.5000 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
CT2  C     250.000     1.4900 ! ALLOW   ALI PEP POL ARO
                ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT2  CA    230.000     1.4900 ! ALLOW   ALI ARO
                ! phe,tyr, JES 8/25/89
CT2  CC    200.000     1.5220 ! ALLOW   POL
                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2  CD    200.000     1.5220 ! ALLOW   POL
                ! adm jr. 5/02/91, acetic acid pure solvent
CT2  CPB   230.000     1.4900 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CT2  CPH1  229.630     1.5000 ! ALLOW ARO
                ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
CT2  CT1   222.500     1.5380 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
CT2  CT2   222.500     1.5300 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
CT3  C     250.000     1.4900 ! ALLOW   ALI PEP POL ARO
                ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT3  CA    230.000     1.4900 ! ALLOW   ALI ARO
                ! toluene, adm jr. 3/7/92
CT3  CC    200.000     1.5220 ! ALLOW   POL
                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT3  CD    200.000     1.5220 ! ALLOW   POL
                ! adm jr. 5/02/91, acetic acid pure solvent
CT3  CPB   230.000     1.4900 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CT3  CPH1  229.630     1.5000 ! ALLOW ARO
                ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
CT3  CS    190.000     1.5310 ! ALLOW   SUL
                ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
CT3  CT1   222.500     1.5380 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
CT3  CT2   222.500     1.5280 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
CT3  CT3   222.500     1.5300 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
CY   CA    350.000     1.3650 ! ALLOW   ARO
                !adm jr., 5/08/91, indole CCDB structure search
CY   CPT   350.000     1.4400 ! ALLOW   ARO
                !adm jr., 12/30/91, for jwk
CY   CT2   230.000     1.5100 ! ALLOW ARO
                !JWK  Kb from alkane freq.. b0 from TRP crystal
FE   CM    258.000     1.9000 ! ALLOW HEM
                ! Heme (6-liganded): CO ligand (KK 05/13/91)
FE   CPM     0.000     3.3814 ! ALLOW HEM
                ! Heme (6-liganded): for "ic para" only (KK 05/13/91)
H    CD    330.000     1.1100 ! ALLOW   PEP POL ARO
                ! adm jr. 5/02/91, acetic acid pure solvent
HA   C     330.000     1.1000 ! ALLOW ARO HEM
                ! Heme vinyl substituent (KK, from propene (JCS))
HA   CA    340.000     1.0830 ! ALLOW ARO
                ! trp, adm jr., 10/02/89
HA   CC    317.130     1.1000 ! ALLOW POL
                ! adm jr., 5/13/91, formamide geometry and vibrations
HA   CP2   309.000     1.1110 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA   CP3   309.000     1.1110 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA   CPM   367.600     1.0900 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
HA   CS    300.000     1.1110 ! ALLOW   SUL
                ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA   CT1   309.000     1.1110 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
HA   CT2   309.000     1.1110 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
HA   CT3   322.000     1.1110 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
HA   CY    330.000     1.0800 ! ALLOW   ARO
                ! JWK 05/14/91 new r0 from indole
HE1  CE1   360.500     1.1000   ! 
		! for propene, yin/adm jr., 12/95
HE2  CE2   365.000     1.1000   ! 
		! for ethene, yin/adm jr., 12/95
HB   CP1   330.000     1.0800 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB   CT1   330.000     1.0800 ! ALLOW   PEP
                ! Alanine Dipeptide ab initio calc's (LK)
HB   CT2   330.000     1.0800 ! ALLOW   PEP
                ! Alanine Dipeptide ab initio calc's (LK)
HB   CT3   330.000     1.0800 ! ALLOW   PEP
                ! Alanine Dipeptide ab initio calc's (LK)
HP   CA    340.000     1.0800 ! ALLOW   ARO
                ! phe,tyr JES 8/25/89
HP   CY    350.000     1.0800 ! ALLOW   ARO
                !adm jr., 12/30/91, for jwk
HR1  CPH1  375.000     1.0830 ! ALLOW ARO
                ! his, adm jr., 6/27/90
HR1  CPH2  340.000     1.0900 ! ALLOW ARO
                ! his, adm jr., 6/28/29
HR2  CPH2  333.000     1.0700 ! ALLOW ARO
                ! his, adm jr., 6/27/90
HR3  CPH1  365.000     1.0830 ! ALLOW ARO
                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
HT   HT      0.000     1.5139 ! ALLOW WAT
                ! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM)
N    C     260.000     1.3000 ! ALLOW PEP POL ARO PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N    CP1   320.000     1.4340 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N    CP3   320.000     1.4550 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC2  C     463.000     1.3650 ! ALLOW   PEP POL ARO
                ! 403.0->463.0, 1.305->1.365 guanidinium (KK)
NC2  CT2   261.000     1.4900 ! ALLOW   ALI POL
                ! arg, (DS)
NC2  CT3   261.000     1.4900 ! ALLOW   ALI POL
                ! methylguanidinium, adm jr., 3/26/92
NC2  HC    455.000     1.0000 ! ALLOW   POL
                ! 405.0->455.0 GUANIDINIUM (KK)
NH1  C     370.000     1.3450 ! ALLOW   PEP POL ARO
                ! Alanine Dipeptide ab initio calc's (LK)
NH1  CT1   320.000     1.4300 ! ALLOW   ALI PEP POL ARO
                ! NMA Gas & Liquid Phase IR Spectra (LK)
NH1  CT2   320.000     1.4300 ! ALLOW   ALI PEP POL ARO
                ! NMA Gas & Liquid Phase IR Spectra (LK)
NH1  CT3   320.000     1.4300 ! ALLOW   ALI PEP POL ARO
                ! NMA Gas & Liquid Phase IR Spectra (LK)
NH1  H     440.000     0.9970 ! ALLOW   PEP POL ARO
                ! Alanine Dipeptide ab initio calc's (LK)
NH1  HC    405.000     0.9800 ! ALLOW   PEP POL ARO
                ! (DS)
NH2  CC    430.000     1.3600 ! ALLOW   PEP POL ARO
                ! adm jr. 4/10/91, acetamide
NH2  CT2   240.000     1.4550
                ! from NH2  CT3, neutral glycine, adm jr.
NH2  CT3   240.000     1.4550 ! ALLOW   POL
                ! methylamine geom/freq, adm jr., 6/2/92
NH2  H     480.000     1.0000 ! ALLOW   POL
                ! adm jr. 8/13/90 acetamide geometry and vibrations
NH2  HC    460.000     1.0000 ! ALLOW   POL
                ! methylamine geom/freq, adm jr., 6/2/92
NH3  CT1   200.000     1.4800 ! ALLOW   ALI POL
                ! new stretch and bend; methylammonium (KK 03/10/92)
NH3  CT2   200.000     1.4800 ! ALLOW   ALI POL
                ! new stretch and bend; methylammonium (KK 03/10/92)
NH3  CT3   200.000     1.4800 ! ALLOW   ALI POL
                ! new stretch and bend; methylammonium (KK 03/10/92)
NH3  HC    403.000     1.0400 ! ALLOW   POL
                ! new stretch and bend; methylammonium (KK 03/10/92)
NP   CP1   320.000     1.4850 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP   CP3   320.000     1.5020 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP   HC    460.000     1.0060 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NPH  CPA   377.200     1.3757 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH  FE    270.200     1.9580 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NR1  CPH1  400.000     1.3800 ! ALLOW ARO
                ! his, ADM JR., 7/20/89
NR1  CPH2  400.000     1.3600 ! ALLOW ARO
                ! his, ADM JR., 7/20/89
NR1  H     466.000     1.0000 ! ALLOW ARO
                ! his, ADM JR., 7/20/89
NR2  CPH1  400.000     1.3800 ! ALLOW ARO
                ! his, ADM JR., 7/20/89
NR2  CPH2  400.000     1.3200 ! ALLOW ARO
                ! his, ADM JR., 7/20/89
NR2  FE     65.000     2.2000 ! ALLOW HEM
                ! Heme (6-liganded): His ligand (KK 05/13/91)
NR3  CPH1  380.000     1.3700 ! ALLOW ARO
                ! his, adm jr., 6/28/90
NR3  CPH2  380.000     1.3200 ! ALLOW ARO
                ! his, adm jr., 6/27/90
NR3  H     453.000     1.0000 ! ALLOW ARO
                ! his, adm jr., 6/27/90
NY   CA    270.000     1.3700 ! ALLOW   ARO
                !adm jr., 12/30/91, for jwk
NY   CPT   270.000     1.3750 ! ALLOW   ARO
                !adm jr., 12/30/91, for jwk
NY   H     465.000     0.9760 ! ALLOW   ARO
                ! indole JWK   08/28/89
O    C     620.000     1.2300 ! ALLOW   PEP POL ARO
                ! Peptide geometry, condensed phase (LK)
O    CC    650.000     1.2300 ! ALLOW   PEP POL ARO
                ! adm jr. 4/10/91, acetamide
OB   CC    750.000     1.2200 ! ALLOW   PEP POL ARO
                ! adm jr., 10/17/90, acetic acid vibrations and geom.
OB   CD    750.000     1.2200 ! ALLOW   PEP POL ARO
                ! adm jr. 5/02/91, acetic acid pure solvent
OC   CA    525.000     1.2600 ! ALLOW   PEP POL ARO ION
                ! adm jr. 8/27/91, phenoxide
OC   CC    525.000     1.2600 ! ALLOW   PEP POL ARO ION
                ! adm jr. 7/23/91, acetic acid
OC   CT2   450.000     1.3300 ! ALLOW   ALC
                ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
OC   CT3   450.000     1.3300 ! ALLOW   ALC
                ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92
OH1  CA    334.300     1.4110 ! ALLOW   ARO ALC
                ! MeOH, EMB 10/10/89,
OH1  CD    230.000     1.4000 ! ALLOW   PEP POL ARO ALC
                ! adm jr. 5/02/91, acetic acid pure solvent
OH1  CT1   428.000     1.4200 ! ALLOW   ALI ALC ARO
                ! methanol vib fit EMB 11/21/89
OH1  CT2   428.000     1.4200 ! ALLOW   ALI ALC ARO
                ! methanol vib fit EMB 11/21/89
OH1  CT3   428.000     1.4200 ! ALLOW   ALI ALC ARO
                ! methanol vib fit EMB 11/21/89
OH1  H     545.000     0.9600 ! ALLOW   ALC ARO
                ! EMB 11/21/89 methanol vib fit
OM   CM   1115.000     1.1280 ! ALLOW HEM
                ! Heme (6-liganded): CO ligand (KK 05/13/91)
OM   FE    250.000     1.8000 ! ALLOW HEM
                ! Heme (6-liganded): O2 ligand (KK 05/13/91)
OM   OM    600.000     1.2300 ! ALLOW HEM
                ! Heme (6-liganded): O2 ligand (KK 05/13/91)
OS   CD    150.000     1.3340 ! ALLOW POL PEP
                ! adm jr. 5/02/91, acetic acid pure solvent
OS   CT3   340.000     1.4300 ! ALLOW POL PEP
                ! adm jr., 4/05/91, for PRES CT1 from methylacetate
OT   HT    450.000     0.9572 ! ALLOW   WAT
                ! FROM TIPS3P GEOM
! Modified for CYG residue after 6-31G** geometry optimization Felix
S    CC   240.000      1.7814 ! ALLOW   ALI SUL ION
!S    CC   240.000      1.8160 ! ALLOW   ALI SUL ION
! Modified for CYG residue
S    CT2   198.000     1.8180 ! ALLOW   ALI SUL ION
                ! fitted to C-S s   9/26/92 (FL)
S    CT3   240.000     1.8160 ! ALLOW   ALI SUL ION
                ! fitted to C-S s   9/26/92 (FL)
S    HS    275.000     1.3250 ! ALLOW   SUL ION
                ! methanethiol pure solvent, adm jr., 6/22/92
SM   CT2   214.000     1.8160 ! ALLOW   SUL ION
                ! improved CSSC dihedral in DMDS  5/15/92 (FL)
SM   CT3   214.000     1.8160 ! ALLOW   SUL ION
                ! improved CSSC dihedral in DMDS  5/15/92 (FL)
SM   SM    173.000     2.0290 ! ALLOW   SUL ION
                ! improved CSSC dihedral in DMDS  5/15/92 (FL)
SS   CS    205.000     1.8360 ! ALLOW   SUL
                ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
CA   ON2b  340.0       1.38    !phenol phosphate, 6/94, adm jr.
ON2b P     270.0       1.61    !phenol phosphate, 6/94, adm jr.

!nucleic acid section
!
!NICH parameters to maintain back compatibility following
!atom type switch from HN3 to HN6
CN3C HN6    374.0       1.09    !nadh/ppi, jjp1/adm jr. 7/95
CN3  HN6    350.0       1.09    !nadh, adm jr., 8/98
!
CN1  CN3    302.0       1.409   !U, adm jr. 11/97
CN1  CN3T   302.0       1.403   !T, adm jr. 11/97
CN1A CN3    302.0       1.480   !nad/ppi, jjp1/adm jr. 7/95
CN1  CN5G   302.0       1.360   !G, adm jr. 11/97
CN1A NN1    560.0       1.360   !nad/ppi, jjp1/adm jr. 7/95
CN1  NN2    380.0       1.367   !C, adm jr. 11/97
CN1T NN2B   302.0       1.348   !U,T adm jr. 11/97
CN1  NN2G   340.0       1.396   !G, adm jr. 11/97
CN1  NN2U   340.0       1.389   !U,T adm jr. 11/97
CN1T NN2U   340.0       1.383   !U,T adm jr. 11/97
CN1  NN3    350.0       1.335   !C, adm jr. 11/97
CN1  ON1    660.0       1.234   !U,A,G par_a4 adm jr. 10/2/91
CN1A ON1    860.0       1.230   !nad/ppi, jjp1/adm jr. 7/95
CN1T ON1    860.0       1.230   !nad/ppi, jjp1/adm jr. 7/95
CN1  ON1C   620.0       1.245   !C, adm jr. 10/2/91
CN2  CN3    320.0       1.406   !C, adm jr. 11/97
CN2  CN3D   260.0       1.405   !5mc, adm jr. 9/9/93, from cn2 cn3
CN2  CN5    360.0       1.358   !A, adm jr. 11/97
CN2  NN1    360.0       1.366   !C,A,G JWK, adm jr. 10/2/91
CN2  NN2G   400.0       1.392   !G  
CN2  NN3    450.0       1.343   !C  
CN2  NN3A   400.0       1.342   !A, adm jr. 11/97
CN2  NN3G   320.0       1.326   !G, adm jr. 11/97
CN3  CN3    500.0       1.326   !C,U adm jr. 11/97
CN3  CN3T   560.0       1.320   !T, adm jr. 11/97
CN3A CN3    450.0       1.360   !nad/ppi, jjp1/adm jr. 7/95
CN3B CN3    420.0       1.350   !nad/ppi, jjp1/adm jr. 7/95
CN3C CN3    420.0       1.320   !nadh/ppi, jjp1/adm jr. 7/95
CN3D CN3    560.0       1.335   !5mc, adm jr. 9/9/93, from cn3 cn3
CN3  CN8    222.5       1.490   !nadh/ppi, jjp1/adm jr. 7/95
CN3D CN9    230.0       1.480   !5mc, adm jr. 9/9/93, from cn3 cn9
CN3T CN9    230.0       1.478   !T, adm jr. 11/97
CN3  HN3    350.0       1.09    !C,U, JWK
CN3T HN3    350.0       1.09    !T, JWK
CN3  HN3B   350.0       1.09    !nad/ppi, jjp1/adm jr. 7/95
CN3A HN3B   350.0       1.09    !nad/ppi, jjp1/adm jr. 7/95
CN3B HN3B   350.0       1.09    !nad/ppi, jjp1/adm jr. 7/95
CN3C HN3    374.0       1.09    !nadh/ppi, jjp1/adm jr. 7/95
CN3  NN2    302.0       1.343   !C, adm jr. 11/97
CN3  NN2B   320.0       1.343   !U,T adm jr. 11/97
CN3B NN2    420.0       1.315   !nad/ppi, jjp1/adm jr. 7/95
CN3C NN2    420.0       1.355   !nadh/ppi, jjp1/adm jr. 7/95
CN4  HN3    380.0       1.09    !G,A, JWK par_a7 9/30/91
CN4  NN2    320.0       1.374   !A, adm jr. 11/97
CN4  NN2B   300.0       1.378   !G, adm jr. 11/97
CN4  NN2G   350.0       1.365   !Inosine, adm jr. 2/94
CN4  NN3A   420.0       1.322   !A, adm jr. 11/97
CN4  NN3I   450.0       1.295   !Inosine, adm jr. 2/94
CN4  NN4    400.0       1.305   !G,A, adm jr. 11/97
CN5  CN5    310.0       1.361   !A, adm jr. 11/97
CN5  CN5G   320.0       1.350   !G, adm jr. 11/97
CN5  NN2    300.0       1.375   !A, adm jr. 11/97
CN5  NN2B   302.0       1.375   !G, adm jr. 11/97
CN5  NN3A   350.0       1.312   !A, JWK par_a8 9/30/91
CN5  NN3G   350.0       1.315   !G, adm jr. 11/97
CN5  NN3I   350.0       1.332   !Inosine, adm jr. 9/98
CN5  NN4    310.0       1.355   !A, adm jr. 11/97
CN5G NN4    310.0       1.365   !G, adm jr. 11/97
CN8  CN8    222.50      1.528   !Alkanes, sacred
CN8  CN9    222.50      1.528   !Alkanes, sacred
CN8  NN2    400.0       1.460   !9-E-GUA, ADM JR.
CN8  ON5    428.0       1.42    !RIBOSE, MeOH
CN9  HN9    322.0       1.111   !alkanes
CN9  ON2    340.0       1.43    !DMP, ADM Jr.
HN1  NN1    488.0       1.00    !A,C,G, JWK, adm jr. 7/24/91
HN2  NN2    474.0       1.01    !C,U, JWK
HN2  NN2B   474.0       1.01    !G, adm jr. 11/97
HN2  NN2G   471.0       1.01    !G, JWK, par_a12 9/30/91
HN2  NN2U   474.0       1.01    !U, JWK, adm jr. 7/24/91
HN4  ON4    545.0       0.960   !MP_1, ADM Jr.
!HT   HT       0.0       1.5139  ! from TIPS3P geometry (for SHAKE w/PARAM)
!HT   OT     450.0       0.9572  ! from TIPS3P geometry
ON2  P      270.0       1.60    !DMP, ADM Jr. 
ON3  P      580.0       1.48    !DMP, ADM Jr.
ON4  P      237.0       1.58    !MP_1, ADM Jr.
ON2  P2     300.0       1.68    !nad/ppi, jjp1/adm jr. 7/95
ON3  P2     480.0       1.53    !nad/ppi, jjp1/adm jr. 7/95
NN5  HN1    460.0       1.01    !sugar model, adm jr.
!@@@@@@@@@ Begining of endocyclic bonds for deoxy-ribose @@@@@@@@@
CN7B ON6    260.0       1.420   ! From exp  
CN7B CN8    200.0       1.518   ! From exp 
CN7  ON6    240.0       1.446   ! Fom exp.
CN7  CN8    222.5       1.516  	! From exp. 
CN7  CN7    222.5       1.529  	! From exp 
CN7  HN7    309.0       1.111   !Alkanes, sacred
CN8  HN8    309.0       1.111   !Alkanes, sacred
CN7B HN7    309.0       1.111   ! From CN8  HN7 (NF)
!@@@@@@@@@ End of endocyclic bonds for deoxy-ribose @@@@@@@@@
!@@@@@@@@@ Begining of endocyclic bonds for ribose @@@@@@@@@
CN7B ON6B   260.0       1.420   ! From CN7B ON6
CN7  ON6B   240.0       1.480   ! From CN7  ON6
CN7B CN7B   200.0       1.450   ! 
CN7  CN7B   222.5       1.460   ! Specific to RNA 
!@@@@@@@@@ End of endocyclic bonds for ribose @@@@@@@@@

!@@@@@@@@@ Begining of endocyclic bonds for arabinose @@@@@@@@@
! Transfered from DNA
CN7B CN7C   200.0       1.518   ! For arabinose, from CN7B CN8
CN7  CN7C   222.5       1.516   ! For arabinose, from CN7  CN8
CN7C HN7    309.0       1.111   ! From CN8  HN7
!@@@@@@@@@ End of endocyclic bonds for arabinose @@@@@@@@@

!@@@@@@@@@ Begining of exocyclic bonds for deoxy-ribose @@@@@@@@@
CN7  CN8B   222.5       1.512   ! From exp. 
CN8B ON2    320.0       1.44    ! From exp
!CN8B ON5    250.0       1.44    ! From CN8B ON2
CN8B ON5    428.0       1.42    !From CN8 ON2, adm jr., 8/30/98
CN7  ON2    310.0       1.433   ! From exp
CN7B ON2    310.0       1.433   ! From exp, for NADPH etc.
!CN7  ON5    250.0       1.420   ! ALLOW   ALI ALC ARO
CN7  ON5    428.0       1.42    !From CN8 ON2, adm jr., 8/30/98
! C1'-N9 (purines)/C1'-N1 (pyrimidines)
CN9  NN2    400.0       1.456   !9-M-A/C, adm jr.
CN8  NN2B   400.0       1.458   !9-M-G/T/U, adm jr.
CN9  NN2B   400.0       1.458   !9-M-G/T/U, adm jr.
CN7B NN2    220.0       1.456   !A/C
CN7B NN2B   220.0       1.458   !G/T/U
! C5'-H in model compounds and DNA
CN8B  HN8    309.0       1.111  !Alkanes, sacred
ON5   HN5    545.0       0.960  !RIBOSE, MeOH
!@@@@@@@@@ End of exocyclic bonds for deoxy-ribose @@@@@@@@@

!@@@@@@@@@ Begining of exocyclic bonds for ribose @@@@@@@@@
!CN7B ON5    250.0       1.400   ! From CN7  ON5
CN7B ON5    428.0       1.400   ! check adm jr., 
!FC should be 428.000 based on Meoh
!@@@@@@@@@ End of exocyclic bonds for ribose @@@@@@@@@

!@@@@@@@@@ Begining of exocyclic bonds for arabinose @@@@@@@@@
!CN7C ON5    250.0       1.400   ! From CN7  ON5
CN7C ON5    428.0       1.400   ! check adm jr.,
!FC should be 428.000 based on Meoh
!@@@@@@@@@ End of exocyclic bonds for arabinose @@@@@@@@@

!@@@@@@@@@ Begining of bonds for nucleotide analogue @@@@@@@@@
CN8  ON2    340.0       1.44    !
!@@@@@@@@@ End of bonds for nucleotide analogue @@@@@@@@@

! C1'-ND1 in imidazole model compound
CN7B NR1    220.000     1.4620  ! From crystal nucleosides A/G (NF)
!NR1  CPH1   400.000     1.3800  ! From imidazole (NF)
!NR1  CPH2   400.000     1.3600  ! From imidazole (NF)
!NR2  CPH1   400.000     1.3800  ! From imidazole (NF)
!NR2  CPH2   400.000     1.3200  ! From imidazole (NF)
!CPH1 CPH1   410.000     1.3600  ! From imidazole (NF)
!HR1  CPH2   340.000     1.0900  ! From imidazole (NF)
!HR3  CPH1   365.000     1.0830  ! From imidazole (NF)

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
!
! from lipids
! from CHARMm23 guessed parameters
! Rommie Jerome
 O    CC   CPH1 31.250 120.250
NH2  CC   CPH1 57.500 115.500
CC   CPH1 CPH1 45.800 130.000
CC   CPH1 NR2 87.900 115.000
CPH1 CPH1 NC2 135.000 108.000 
NR1  CPH1 NC2 62.794 120.765
CPH1 NC2  C 62.300 120.000
CN7  CN7  CTL3 60.000 100.000
ON6B CN7  CTL3 100.000 110.000
CTL3 CN7  HN7 37.265 109.050
CN7  CTL3 OSL 40.241 109.761
CN7  CTL3 HAL3  36.106 110.260
NC2  C    HC 60.100 118.185
NC2  CT2  C 53.800 108.167
CT2  C    CT2 70.000 121.500
C    CT2  OH1 75.700 110.100
CT2  CT2  CTL3 58.070 111.520
OH1  CT2  CTL3 73.56 112.480
CTL3 CT2  HA 36.790 109.664
CT2  CTL3 OSL 40.241 109.761
CT2  CTL3 HAL3 36.106 110.260
! END OF CHARMM-GUESSED PARAMETERS

! Modified for CYG residue after 6-31G** geometry optimization Felix
CT2  S    CC    34.000    100.2000 ! ALLOW   ALI SUL ION

CT2  CC   S     34.000    114.5000 ! ALLOW   ALI SUL ION

O    CC   S     34.000    122.2000 ! ALLOW   ALI SUL ION
! End of optimization Felix

!lipids section
OBL  CL   CTL3    70.0     125.0     20.0   2.442  ! methyl acetate
OBL  CL   CTL2    70.0     125.0     20.0   2.442  ! methyl acetate
OBL  CL   CTL1    70.0     125.0     20.0   2.442  ! methyl acetate
OSL  CL   OBL     90.0     125.9    160.0   2.2576 ! acetic acid
CL   OSL  CTL1    40.0     109.6     30.0   2.2651 ! methyl acetate
CL   OSL  CTL2    40.0     109.6     30.0   2.2651 ! methyl acetate
CL   OSL  CTL3    40.0     109.6     30.0   2.2651 ! methyl acetate
HAL2 CTL2 CL      33.00    109.50   30.00   2.163  ! methyl acetate
HAL3 CTL3 CL      33.00    109.50   30.00   2.163  ! methyl acetate
CTL2 CTL2 CL      52.0     108.00   ! alkane
CTL3 CTL2 CL      52.0     108.00   ! alkane
OSL  CL   CTL3    55.0     109.0    20.00   2.3260 ! methyl acetate
OSL  CL   CTL2    55.0     109.0    20.00   2.3260 ! methyl acetate
OHL  CL   OBL     50.0     123.0    210.0   2.2620 ! acetic acid
OCL  CL   CTL2    40.0     118.0     50.0   2.3880 ! acetate
OCL  CL   CTL3    40.0     118.0     50.0   2.3880 ! acetate
OCL  CL   OCL    100.0     124.0     70.0   2.2250 ! acetate
OHL  CL   CTL3    55.0     110.50   ! acetic acid
OHL  CL   CTL2    55.0     110.50   ! acetic acid
HOL  OHL  CL     55.0      115.0    ! acetic acid
OSL  CTL1 CTL2   75.700    110.10   ! acetic acid
OSL  CTL1 CTL3   75.700    110.10   ! acetic acid
OSL  CTL2 CTL1   75.700    110.10   ! acetic acid
OSL  CTL2 CTL2   75.700    110.10   ! acetic acid
OSL  CTL2 CTL3   75.700    110.10   ! acetic acid
HAL2 CTL2 HAL2   35.500    109.00    5.40   1.80200 ! alkane, 3/92
HAL3 CTL3 HAL3   35.500    108.40    5.40   1.80200 ! alkane, 3/92
HAL1 CTL1 OSL    60.0      109.5    ! phosphate
HAL2 CTL2 OSL    60.0      109.5    ! phosphate
HAL3 CTL3 OSL    60.0      109.5    ! phosphate
CTL2 OSL  PL     20.0      120.0    35.0    2.33   ! phosphate
CTL3 OSL  PL     20.0      120.0    35.0    2.33   ! phosphate
HOL  OHL  PL     30.0      115.0    40.0    2.30   ! phosphate
OSL  PL   OSL    80.0      104.3    ! phosphate
OSL  PL   O2L    98.9      111.6    ! phosphate
OSL  PL   OHL    48.1      108.0    ! phosphate
O2L  PL   O2L   120.0      120.0    ! phosphate
O2L  PL   OHL    98.9      108.23   ! phosphate
NTL  CTL2 HL     40.0      109.5    27.     2.13   ! tetramethylammonium
NTL  CTL5 HL     40.0      109.5    27.     2.13   ! tetramethylammonium
HL   CTL2 HL     24.0      109.50   28.     1.767  ! tetramethylammonium
HL   CTL5 HL     24.0      109.50   28.     1.767  ! tetramethylammonium
CTL5 NTL  CTL2   60.0      109.5    26.     2.466  ! tetramethylammonium
CTL5 NTL  CTL5   60.0      109.5    26.     2.466  ! tetramethylammonium
HL   CTL2 CTL2   33.430    110.10   22.53   2.179  ! alkane
HL   CTL2 CTL3   33.430    110.10   22.53   2.179  ! alkane
HAL1 CTL1 CTL1   34.500    110.10   22.53   2.179  ! alkane, 3/92
HAL1 CTL1 CTL2   34.500    110.10   22.53   2.179  ! alkane, 3/92
HAL1 CTL1 CTL3   34.500    110.10   22.53   2.179  ! alkane, 3/92
HAL2 CTL2 CTL1   26.500    110.10   22.53   2.179  ! alkane, 4/98
HAL2 CTL2 CTL2   26.500    110.10   22.53   2.179  ! alkane, 4/98
HAL2 CTL2 CTL3   34.600    110.10   22.53   2.179  ! alkane, 4/98
HAL3 CTL3 CTL1   33.430    110.10   22.53   2.179  ! alkane, 4/98
HAL3 CTL3 CTL2   34.600    110.10   22.53   2.179  ! alkane, 4/98
HAL3 CTL3 CTL3   37.500    110.10   22.53   2.179  ! alkane, 4/98
NTL  CTL2 CTL2   67.7      115.00   ! tetramethylammonium
NTL  CTL2 CTL3   67.7      115.00   ! tetramethylammonium
HCL  NH3L CTL2   33.0      109.50    4.00   2.056  ! ethanolamine
HCL  NH3L HCL    41.0      109.50   ! ethanolamine
NH3L CTL2 CTL2   67.7      110.00   ! ethanolamine
NH3L CTL2 HAL2   45.0      107.50   35.00   2.0836 ! ethanolamine
CTL1 CTL1 CTL1   53.350    111.00    8.00   2.561  ! alkane, 3/92
CTL1 CTL1 CTL2   58.350    113.50   11.16   2.561  ! glycerol
CTL1 CTL1 CTL3   53.350    108.50    8.00   2.561  ! alkane, 3/92
CTL1 CTL2 CTL1   58.350    113.50   11.16   2.561  ! glycerol
CTL1 CTL2 CTL2   58.350    113.50   11.16   2.561  ! glycerol
CTL1 CTL2 CTL3   58.350    113.50   11.16   2.561  ! glycerol
CTL2 CTL1 CTL2   58.350    113.50   11.16   2.561  ! glycerol
CTL2 CTL1 CTL3   58.350    113.50   11.16   2.561  ! glycerol
CTL2 CTL2 CTL2   58.350    113.60   11.16   2.561  ! alkane, 3/92
CTL2 CTL2 CTL3   58.000    115.00    8.00   2.561  ! alkane, 3/92
HOL  OHL  CTL1   57.500    106.00   ! glycerol
HOL  OHL  CTL2   57.500    106.00   ! glycerol
HOL  OHL  CTL3   57.500    106.00   ! glycerol
OHL  CTL1 CTL2   75.700    110.10   ! glycerol
OHL  CTL2 CTL1   75.700    110.10   ! glycerol
OHL  CTL2 CTL2   75.700    110.10   ! glycerol
OHL  CTL2 CTL3   75.700    110.10   ! glycerol
OHL  CTL1 HAL1   45.900    108.89   ! glycerol
OHL  CTL2 HAL2   45.900    108.89   ! glycerol
OHL  CTL3 HAL3   45.900    108.89   ! glycerol
O2L  SL   O2L   130.0      109.47  35.0    2.45 ! methylsulfate
O2L  SL   OSL    85.0       98.0                ! methylsulfate
CTL2 OSL  SL     15.0      109.0   27.00   1.90 ! methylsulfate
CTL3 OSL  SL     15.0      109.0   27.00   1.90 ! methylsulfate
!HT   OT   HT     55.0      104.52   ! FROM TIPS3P GEOMETRY
CEL1 CEL1 CTL2   48.00     123.50   ! from 2-butene, yin,adm jr., 12/95
CEL1 CEL1 CTL3   48.00     123.50   ! 2-butene, yin,adm jr., 12/95
CEL2 CEL1 CTL2   48.00     126.00   ! 1-butene; from propene, yin,adm jr., 12/95
CEL2 CEL1 CTL3   47.00     125.20   ! propene, yin,adm jr., 12/95
HEL1 CEL1 CEL1   52.00     119.50   ! 2-butene, yin,adm jr., 12/95
HEL1 CEL1 CEL2   42.00     118.00   ! propene, yin,adm jr., 12/95
HEL1 CEL1 CTL2   40.00     116.00   ! 1-butene; from propene, yin,adm jr., 12/95
HEL1 CEL1 CTL3   22.00     117.00   ! propene, yin,adm jr., 12/95
HEL2 CEL2 CEL1   45.00     120.50   ! propene, yin,adm jr., 12/95
HEL2 CEL2 CEL2   55.50     120.50   ! ethene, yin,adm jr., 12/95
HEL2 CEL2 HEL2   19.00     119.00   ! propene, yin,adm jr., 12/95
CEL1 CTL2 CTL2   32.00     112.20   ! 1-butene; from propene, yin,adm jr., 12/95
CEL1 CTL2 CTL3   32.00     112.20   ! 1-butene; from propene, yin,adm jr., 12/95
HAL2 CTL2 CEL1   45.00     111.50   ! 1-butene; from propene, yin,adm jr., 12/95
HAL3 CTL3 CEL1   42.00     111.50   ! 2-butene, yin,adm jr., 12/95
!
CA   CA   CA    40.000    120.00   35.00   2.41620 ! ALLOW   ARO
                ! JES 8/25/89
CE1  CE1  CT3    48.00    123.50   ! 
		! for 2-butene, yin/adm jr., 12/95
CE1  CT2  CT3    32.00    112.20   ! 
		! for 1-butene; from propene, yin/adm jr., 12/95
CE2  CE1  CT2    48.00    126.00   ! 
		! for 1-butene; from propene, yin/adm jr., 12/95
CE2  CE1  CT3    47.00    125.20   ! 
		! for propene, yin/adm jr., 12/95
CP1  N    C      60.000   117.0000 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2  CP1  C      52.000   112.3000 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2  CP1  CC     52.000   112.3000 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2  CP1  CD     50.000   112.3000 ! ALLOW PRO PEP
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2  CP2  CP1    70.000   108.5000 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3  CP2  CP2    70.000   108.5000 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3  N    C      60.000   117.0000 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3  N    CP1   100.000   114.2000 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3  NP   CP1   100.000   111.0000 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CPA  CPB  C      70.000   126.7400 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CPA  CPM  CPA    94.200   125.1200 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPA  NPH  CPA   139.300   103.9000 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB  C    C      70.000   121.5000 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CPB  CPB  C      70.000   126.7500 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CPB  CPB  CPA    30.800   106.5100 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPH2 NR1  CPH1  130.000   107.5000 ! ALLOW ARO
                ! his, adm jr., 6/27/90
CPH2 NR2  CPH1  130.000   104.0000 ! ALLOW ARO
                ! his, adm jr., 6/27/90
CPH2 NR3  CPH1  145.000   108.0000 ! ALLOW ARO
                ! his, ADM JR., 7/20/89
CPM  CPA  CPB    61.600   124.0700 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPT  CA   CA     60.000   118.0000 ! ALLOW   ARO
                !adm jr., 12/30/91, for jwk
CPT  CPT  CA     60.000   122.0000 ! ALLOW   ARO
                !adm jr., 12/30/91, for jwk
CPT  CY   CA   120.000    107.40   25.00   2.26100 ! ALLOW   ARO
                !adm jr., 12/30/91, for jwk
CPT  NY   CA    110.000   108.0000 ! ALLOW   ARO
                !adm jr., 12/30/91, for jwk
CT1  CT1  C      52.000   108.0000 ! ALLOW   ALI PEP POL ARO
                ! Alanine Dipeptide ab initio calc's (LK)
CT1  CT1  CC     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1  CT1  CT1   53.350    111.00    8.00   2.56100 ! ALLOW ALI
                ! alkane update, adm jr., 3/2/92
CT1  CT2  CA     51.800   107.5000 ! ALLOW   ALI ARO
                ! PARALLH19 (JES)
CT1  CT2  CC     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1  CT2  CD     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
                ! adm jr. 5/02/91, acetic acid pure solvent
CT1  CT2  CPH1   58.350   113.0000 ! ALLOW ARO
                ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted
CT1  CT2  CT1   58.350    113.50   11.16   2.56100 ! ALLOW   ALI
                ! alkane frequencies (MJF), alkane geometries (SF)
CT1  NH1  C      50.000   120.0000 ! ALLOW   ALI PEP POL ARO
                ! NMA Vib Modes (LK)
CT2  CA   CA     45.800   122.3000 ! ALLOW   ALI ARO
                ! PARALLH19 (JES)
CT2  CPB  CPA    65.000   126.7400 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CT2  CPB  CPB    65.000   126.7500 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CT2  CPH1 CPH1   45.800   130.0000 ! ALLOW ARO
                ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS
CT2  CT1  C      52.000   108.0000 ! ALLOW   ALI PEP POL ARO
                ! Alanine Dipeptide ab initio calc's (LK)
CT2  CT1  CC     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2  CT1  CD     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
                ! adm jr. 5/02/91, acetic acid pure solvent
CT2  CT1  CT1   53.350    111.00    8.00   2.56100 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
CT2  CT2  C      52.000   108.0000 ! ALLOW   ALI PEP POL ARO
                ! from CT2  CT1  C, for lactams, adm jr.
CT2  CT2  CC     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2  CT2  CD     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
                ! adm jr. 5/02/91, acetic acid pure solvent
CT2  CT2  CPB    70.000   113.0000 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CT2  CT2  CT1   58.350    113.50   11.16   2.56100 ! ALLOW   ALI
                ! alkane frequencies (MJF), alkane geometries (SF)
CT2  CT2  CT2   58.350    113.60   11.16   2.56100 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
CT2  CT3  CT1   58.350    113.50   11.16   2.56100 ! ALLOW   ALI
                ! alkane frequencies (MJF), alkane geometries (SF)
CT2  CY   CA     45.800   129.4000 ! ALLOW ARO
                !adm jr., 5/08/91,  indole CCDB structure search
CT2  CY   CPT    45.800   124.0000 ! ALLOW ARO
                !adm jr., 5/08/91,  indole CCDB structure search
CT2  NC2  C      62.300   120.0000 ! ALLOW   ALI POL PEP ARO
                ! 107.5->120.0 to make planar Arg (KK)
CT2  NH1  C      50.000   120.0000 ! ALLOW   ALI PEP POL ARO
                ! NMA Vib Modes (LK)
CT2  OS   CD    40.000    109.60   30.00   2.26510 ! ALLOW  POL PEP
                ! adm jr. 5/02/91, acetic acid pure solvent
CT3  CA   CA     45.800   122.3000 ! ALLOW   ALI ARO
                ! toluene, adm jr., 3/7/92
CT3  CPB  CPA    65.000   126.7400 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CT3  CPB  CPB    65.000   126.7500 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
CT3  CPH1 CPH1   45.800   130.0000 ! ALLOW ARO
                ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS
CT3  CT1  C      52.000   108.0000 ! ALLOW   ALI PEP POL ARO
                ! Alanine Dipeptide ab initio calc's (LK)
CT3  CT1  CC     52.000   108.0000 ! ALLOW   ALI PEP POL ARO
                ! adm jr. 4/09/92, for ALA cter
CT3  CT1  CT1   53.350    108.50    8.00   2.56100 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
CT3  CT1  CT2   53.350    114.00    8.00   2.56100 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
CT3  CT1  CT3   53.350    114.00    8.00   2.56100 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
CT3  CT2  CA     51.800   107.5000 ! ALLOW   ALI ARO
                ! ethylbenzene, adm jr., 3/7/92
CT3  CT2  CPH1   58.350   113.0000 ! ALLOW ARO
                ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted
CT3  CT2  CT1   58.350    113.50   11.16   2.56100 ! ALLOW   ALI
                ! alkane frequencies (MJF), alkane geometries (SF)
CT3  CT2  CT2   58.000    115.00    8.00   2.56100 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
CT3  CT2  CT3   53.350    114.00    8.00   2.56100 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
CT3  NC2  C      62.300   120.0000 ! ALLOW   ALI POL PEP ARO
                ! methylguanidinium, adm jr., 3/26/92
CT3  NH1  C      50.000   120.0000 ! ALLOW   ALI PEP POL ARO
                ! NMA Vib Modes (LK)
CT3  OS   CD    40.000    109.60   30.00   2.26510 ! ALLOW  POL PEP
                ! adm jr. 5/02/91, acetic acid pure solvent
CT3  S    CT2    34.000    95.0000 ! ALLOW   ALI SUL ION
! Modified for CYG residue
!CT2  S    CC    34.000    95.0000 ! ALLOW   ALI SUL ION
                ! expt. MeEtS,    3/26/92 (FL)
CY   CPT  CA    160.000   130.6000 ! ALLOW   ARO
                !adm jr., 12/30/91, for jwk
CY   CPT  CPT   110.000   107.4000 ! ALLOW   ARO
                !adm jr., 12/30/91, for jwk
CY   CT2  CT1    58.350   114.0000 ! ALLOW ARO
                ! from TRP crystal, JWK
CY   CT2  CT3    58.350   114.0000 ! ALLOW ARO
                ! from TRP crystal, JWK
FE   NPH  CPA    96.150   128.0500 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
FE   NR2  CPH1   30.000   133.0000 ! ALLOW HEM
                ! Heme (6-liganded): ligand links (KK 05/13/91)
FE   NR2  CPH2   30.000   123.0000 ! ALLOW HEM
                ! Heme (6-liganded): ligand links (KK 05/13/91)
H    NH1  C      34.000   123.0000 ! ALLOW   PEP POL ARO
                ! NMA Vib Modes (LK)
H    NH1  CT1    35.000   117.0000 ! ALLOW   PEP POL ARO ALI
                ! NMA Vibrational Modes (LK)
H    NH1  CT2    35.000   117.0000 ! ALLOW   PEP POL ARO ALI
                ! NMA Vibrational Modes (LK)
H    NH1  CT3    35.000   117.0000 ! ALLOW   PEP POL ARO ALI
                ! NMA Vibrational Modes (LK)
H    NH2  CC     50.000   120.0000 ! ALLOW   POL PEP ARO
                ! his, adm jr. 8/13/90 acetamide geometry and vibrations
H    NH2  H      23.000   120.0000 ! ALLOW   POL
                ! adm jr. 8/13/90 acetamide geometry and vibrations
H    NR1  CPH1  30.000    125.50   20.00   2.15000 ! ALLOW ARO
                ! his, adm jr., 6/27/90
H    NR1  CPH2  30.000    127.00   20.00   2.14000 ! ALLOW ARO
                ! his, adm jr., 6/27/90
H    NR3  CPH1  25.000    126.00   15.00   2.13000 ! ALLOW ARO
                ! his, adm jr., 6/27/90
H    NR3  CPH2  25.000    126.00   15.00   2.09000 ! ALLOW ARO
                ! his, adm jr., 6/27/90
H    NY   CA     28.000   126.0000 ! ALLOW   ARO
                !adm jr., 12/30/91, for jwk
H    NY   CPT    28.000   126.0000 ! ALLOW   ARO
                !adm jr., 12/30/91, for jwk
H    OH1  CA     65.000   108.0000 ! ALLOW   ALC ARO
                ! JES 8/25/89 phenol
H    OH1  CD     55.000   115.0000 ! ALLOW   ALC ARO PEP POL
                ! adm jr. 5/02/91, acetic acid pure solvent
H    OH1  CT1    57.500   106.0000 ! ALLOW   ALC ARO ALI
                ! methanol vib fit EMB 11/21/89
H    OH1  CT2    57.500   106.0000 ! ALLOW   ALC ARO ALI
                ! methanol vib fit EMB 11/21/89
H    OH1  CT3    57.500   106.0000 ! ALLOW   ALC ARO ALI
                ! methanol vib fit EMB 11/21/89
HA   C    C      50.000   120.5000 ! ALLOW   PEP POL ARO
                ! Heme vinyl substituent (KK from propene (JCS))
HA   C    CPB    50.000   120.0000 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
HA   C    HA     50.000   118.0000 ! ALLOW   PEP POL ARO
                ! Heme vinyl substituent (KK from propene (JCS))
HA   CA   CA    29.000    120.00   25.00   2.15250 ! ALLOW ARO
                ! trp, adm jr., 10/02/89
HA   CA   CPT    41.000   122.0000 ! ALLOW   ARO
                !adm jr., 5/08/91, indole CCDB structure search
HA   CA   CY    32.000    125.00   25.00   2.17300 ! ALLOW   ARO
                ! JWK 05/14/91 new theta0 and r0UB from indole
HA   CP2  CP1   33.430    110.10   22.53   2.17900 ! ALLOW ALI PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA   CP2  CP2   26.500    110.10   22.53   2.17900 ! ALLOW ALI PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA   CP2  CP3   26.500    110.10   22.53   2.17900 ! ALLOW ALI PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA   CP2  HA    35.500    109.00    5.40   1.80200 ! ALLOW ALI PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA   CP3  CP2   26.500    110.10   22.53   2.17900 ! ALLOW ALI PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA   CP3  HA    35.500    109.00    5.40   1.80200 ! ALLOW ALI PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA   CPM  CPA    12.700   117.4400 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
HA   CPM  FE      0.000   180.0000 ! ALLOW HEM
                ! Heme (6-liganded): for "ic para" only (KK 05/13/91)
HA   CS   CT3   34.600    110.10   22.53   2.17900 ! ALLOW SUL
                ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA   CS   HA    35.500    108.40   14.00   1.77500 ! ALLOW SUL
                ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA   CT1  C     33.000    109.50   30.00   2.16300 ! ALLOW   ALI PEP POL ARO
                ! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA   CT1  CD    33.000    109.50   30.00   2.16300 ! ALLOW   ALI PEP POL ARO
                ! adm jr. 5/02/91, acetic acid pure solvent
HA   CT1  CT1   34.500    110.10   22.53   2.17900 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
HA   CT1  CT2   34.500    110.10   22.53   2.17900 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
HA   CT1  CT3   34.500    110.10   22.53   2.17900 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
HA   CT1  HA    35.500    109.00    5.40   1.80200 ! TEST for test cpd
                ! based on HA   CT2  HA
HA   CT2  C     33.000    109.50   30.00   2.16300 ! ALLOW   ALI PEP POL ARO
                ! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA   CT2  CA     49.300   107.5000 ! ALLOW   ALI ARO
                ! PARALLH19 (JES)
HA   CT2  CC    33.000    109.50   30.00   2.16300 ! ALLOW   ALI PEP POL ARO
                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HA   CT2  CD    33.000    109.50   30.00   2.16300 ! ALLOW   ALI PEP POL ARO
                ! adm jr. 5/02/91, acetic acid pure solvent
HA   CT2  CE1    45.00    111.50   ! 
		! for 1-butene; from propene, yin/adm jr., 12/95
HA   CT2  CPB    50.000   109.5000 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
HA   CT2  CPH1   33.430   109.5000 ! ALLOW ARO
                ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
HA   CT2  CT1   33.430    110.10   22.53   2.17900 ! ALLOW   ALI
                ! alkane frequencies (MJF), alkane geometries (SF)
HA   CT2  CT2   26.500    110.10   22.53   2.17900 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
HA   CT2  CT3   34.600    110.10   22.53   2.17900 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
HA   CT2  CY     33.430   109.5000 ! ALLOW ARO
                ! ADM JR., 10/02/89, from CT2CT2HA (U-B OMITTED), FOR JOANNA
HA   CT2  HA    35.500    109.00    5.40   1.80200 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
HA   CT3  C     33.000    109.50   30.00   2.16300 ! ALLOW   ALI PEP POL ARO
                ! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA   CT3  CA     49.300   107.5000 ! ALLOW   ALI ARO
                ! toluene, adm jr. 3/7/92
HA   CT3  CC    33.000    109.50   30.00   2.16300 ! ALLOW   ALI PEP POL ARO
                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HA   CT3  CD    33.000    109.50   30.00   2.16300 ! ALLOW   ALI PEP POL ARO
                ! adm jr. 5/02/91, acetic acid pure solvent
HA   CT3  CE1    42.00    111.50   ! 
		! for 2-butene, yin/adm jr., 12/95
HA   CT3  CPB    50.000   109.5000 ! ALLOW HEM
                ! Heme (6-liganded): substituents (KK 05/13/91)
HA   CT3  CPH1   33.430   109.5000 ! ALLOW ARO
                ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
HA   CT3  CS    34.600    110.10   22.53   2.17900 ! ALLOW SUL
                ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA   CT3  CT1   33.430    110.10   22.53   2.17900 ! ALLOW   ALI
                ! alkane frequencies (MJF), alkane geometries (SF)
HA   CT3  CT2   34.600    110.10   22.53   2.17900 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
HA   CT3  CT3   37.500    110.10   22.53   2.17900 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
HA   CT3  HA    35.500    108.40    5.40   1.80200 ! ALLOW   ALI
                ! alkane update, adm jr., 3/2/92
HA   CY   CA    20.000    126.40   25.00   2.18600 ! ALLOW   ARO
                ! JWK 05/14/91 new theta0 and r0UB from indole
HA   CY   CPT   32.000    126.40   25.00   2.25500 ! ALLOW   ARO
                ! JWK 05/14/91 new theta0 and r0UB from indole
HE1  CE1  CE1    52.00    119.50   ! 
		! for 2-butene, yin/adm jr., 12/95
HE1  CE1  CE2    42.00    118.00   ! 
		! for propene, yin/adm jr., 12/95
HE1  CE1  CT2    40.00    116.00   ! 
		! for 1-butene; from propene, yin/adm jr., 12/95
HE1  CE1  CT3    22.00    117.00   ! 
		! for propene, yin/adm jr., 12/95
HE2  CE2  CE1    45.00    120.50   ! 
		! for propene, yin/adm jr., 12/95
HE2  CE2  CE2    55.50    120.50   ! 
		! for ethene, yin/adm jr., 12/95
HE2  CE2  HE2    19.00    119.00   ! 
		! for propene, yin/adm jr., 12/95
HB   CP1  C      50.000   112.0000 ! ALLOW PEP PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB   CP1  CC     50.000   112.0000 ! ALLOW PEP PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB   CP1  CD     50.000   112.0000 ! ALLOW PEP POL PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB   CP1  CP2    35.000   118.0000 ! ALLOW PEP PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB   CT1  C      50.000   109.5000 ! ALLOW  PEP
                ! Alanine Dipeptide ab initio calc's (LK)
HB   CT1  CC     50.000   109.5000 ! ALLOW  PEP POL
                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HB   CT1  CD     50.000   109.5000 ! ALLOW  PEP POL
                ! adm jr. 5/02/91, acetic acid pure solvent
HB   CT1  CT1    35.000   111.0000 ! ALLOW  PEP
                ! Alanine Dipeptide ab initio calc's (LK)
HB   CT1  CT2    35.000   111.0000 ! ALLOW  PEP
                ! Alanine Dipeptide ab initio calc's (LK)
HB   CT1  CT3    35.000   111.0000 ! ALLOW  PEP
                ! Alanine Dipeptide ab initio calc's (LK)
HB   CT2  C      50.000   109.5000 ! ALLOW  PEP
                ! Alanine Dipeptide ab initio calc's (LK)
HB   CT2  CC     50.000   109.5000 ! ALLOW  PEP POL
                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HB   CT2  CD     50.000   109.5000 ! ALLOW  PEP POL
                ! adm jr. 5/02/91, acetic acid pure solvent
HB   CT2  HB     36.000   115.0000 ! ALLOW   PEP
                ! Alanine Dipeptide ab initio calc's (LK)
HB   CT3  C      50.000   109.5000 ! ALLOW  PEP
                ! Alanine Dipeptide ab initio calc's (LK)
HC   NC2  C      49.000   120.0000 ! ALLOW   POL PEP ARO
                ! 35.3->49.0 GUANIDINIUM (KK)
HC   NC2  CT2    40.400   120.0000 ! ALLOW   POL ALI
                ! 107.5->120.0 to make planar Arg (KK)
HC   NC2  CT3    40.400   120.0000 ! ALLOW   POL ALI
                ! methylguanidinium, adm jr., 3/26/92
HC   NC2  HC     25.000   120.0000 ! ALLOW   POL
                ! 40.0->25.0 GUANIDINIUM (KK)
HC   NH2  CT2    50.000   111.0000 ! ALLOW   POL
                ! from HC NH2 CT3, neutral glycine, adm jr.
HC   NH2  CT3    50.000   111.0000 ! ALLOW   POL
                ! methylamine geom/freq, adm jr., 6/2/92
HC   NH2  HC     39.000   106.5000 ! ALLOW   POL
                ! 40.0->25.0 GUANIDINIUM (KK)
HC   NH3  CT1   30.000    109.50   20.00   2.07400 ! ALLOW   POL ALI
                ! new stretch and bend; methylammonium (KK 03/10/92)
HC   NH3  CT2   30.000    109.50   20.00   2.07400 ! ALLOW   POL ALI
                ! new stretch and bend; methylammonium (KK 03/10/92)
HC   NH3  CT3   30.000    109.50   20.00   2.07400 ! ALLOW   POL ALI
                ! new stretch and bend; methylammonium (KK 03/10/92)
HC   NH3  HC     44.000   109.5000 ! ALLOW   POL
                ! new stretch and bend; methylammonium (KK 03/10/92)
HC   NP   CP1   33.000    109.50    4.00   2.05600 ! ALLOW POL ALI PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HC   NP   CP3   33.000    109.50    4.00   2.05600 ! ALLOW POL ALI PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HC   NP   HC     51.000   107.5000 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HP   CA   CA    30.000    120.00   22.00   2.15250 ! ALLOW   ARO
                ! JES 8/25/89 benzene
HP   CA   CPT   30.000    122.00   22.00   2.14600 ! ALLOW   ARO
                !adm jr., 12/30/91, for jwk
HP   CA   CY    32.000    125.00   25.00   2.17300 ! ALLOW   ARO
                ! JWK 05/14/91 new theta0 and r0UB from indole
HP   CY   CA    32.000    126.40   25.00   2.18600 ! ALLOW   ARO
                !adm jr., 12/30/91, for jwk
HP   CY   CPT   32.000    126.40   25.00   2.25500 ! ALLOW   ARO
                ! JWK 05/14/91 new theta0 and r0UB from indole
HR1  CPH1 CPH1  22.000    130.00   15.00   2.21500 ! ALLOW ARO
                ! adm jr., 6/27/90, his
HR3  CPH1 CPH1  25.000    130.00   20.00   2.20000 ! ALLOW ARO
                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
HS   S    CT2    38.800    95.0000 ! ALLOW   SUL ION ALI
                ! methanethiol pure solvent, adm jr., 6/22/92
HS   S    CT3    43.000    95.0000 ! ALLOW   SUL ION ALI
                ! methanethiol pure solvent, adm jr., 6/22/92
HT   OT   HT     55.000   104.5200 ! ALLOW WAT
                ! TIP3P GEOMETRY, ADM JR.
N    C    CP1    20.000   112.5000 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N    C    CT1    20.000   112.5000 ! ALLOW ALI PEP POL ARO PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N    C    CT2    20.000   112.5000 ! ALLOW ALI PEP POL ARO PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N    C    CT3    20.000   112.5000 ! ALLOW ALI PEP POL ARO PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N    CP1  C      50.000   108.2000 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N    CP1  CC     50.000   108.2000 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N    CP1  CD     50.000   108.2000 ! ALLOW PRO PEP
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N    CP1  CP2    70.000   110.8000 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N    CP1  HB     48.000   112.0000 ! ALLOW PEP PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N    CP3  CP2    70.000   110.5000 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N    CP3  HA     48.000   108.0000 ! ALLOW PEP PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC2  C    NC2   52.000    120.00   90.00   2.36420 ! ALLOW   POL PEP ARO
                ! changed from 60.0/120.3 for guanidinium (KK)
NC2  CT2  CT2    67.700   107.5000 ! ALLOW   ALI POL
                ! arg, (DS)
NC2  CT2  HA     51.500   107.5000 ! ALLOW   ALI POL
                ! arg, (DS)
NC2  CT3  HA     51.500   107.5000 ! ALLOW   ALI POL
                ! methylguanidinium, adm jr., 3/26/92
NH1  C    CP1    80.000   116.5000 ! ALLOW PEP PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH1  C    CT1    80.000   116.5000 ! ALLOW   ALI PEP POL ARO
                ! NMA Vib Modes (LK)
NH1  C    CT2    80.000   116.5000 ! ALLOW   ALI PEP POL ARO
                ! NMA Vib Modes (LK)
NH1  C    CT3    80.000   116.5000 ! ALLOW   ALI PEP POL ARO
                ! NMA Vib Modes (LK)
NH1  CT1  C      50.000   107.0000 ! ALLOW   PEP POL ARO ALI
                ! Alanine Dipeptide ab initio calc's (LK)
NH1  CT1  CC     50.000   107.0000 ! ALLOW   PEP POL ARO ALI
                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
NH1  CT1  CD     50.000   107.0000 ! ALLOW   PEP POL ARO ALI
                ! adm jr. 5/02/91, acetic acid pure solvent
NH1  CT1  CT1    70.000   113.5000 ! ALLOW   ALI PEP POL ARO
                ! Alanine Dipeptide ab initio calc's (LK)
NH1  CT1  CT2    70.000   113.5000 ! ALLOW   ALI PEP POL ARO
                ! Alanine Dipeptide ab initio calc's (LK)
NH1  CT1  CT3    70.000   113.5000 ! ALLOW   ALI PEP POL ARO
                ! Alanine Dipeptide ab initio calc's (LK)
NH1  CT1  HB     48.000   108.0000 ! ALLOW PEP
                ! Alanine Dipeptide ab initio calc's (LK)
NH1  CT2  C      50.000   107.0000 ! ALLOW   PEP POL ARO ALI
                ! Alanine Dipeptide ab initio calc's (LK)
NH1  CT2  CC     50.000   107.0000 ! ALLOW   PEP POL ARO ALI
                ! adm jr. 5/20/92, for asn,asp,gln,glu and cters
NH1  CT2  CD     50.000   107.0000 ! ALLOW   PEP POL ARO ALI
                ! adm jr. 5/02/91, acetic acid pure solvent
NH1  CT2  CT2    70.000   113.5000 ! ALLOW   ALI PEP POL ARO
                ! from NH1  CT1  CT2, for lactams, adm jr.
NH1  CT2  HA     51.500   109.5000 ! ALLOW   ALI PEP POL ARO
                ! from NH1  CT3  HA, for lactams, adm jr.
NH1  CT2  HB     48.000   108.0000 ! ALLOW PEP
                ! Alanine Dipeptide ab initio calc's (LK)
NH1  CT3  HA     51.500   109.5000 ! ALLOW   ALI PEP POL ARO
                ! NMA crystal (JCS)
NH2  CC   CP1    80.000   112.5000 ! ALLOW ALI PEP POL ARO PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH2  CC   CT1   50.000    116.50   50.00   2.45000 ! ALLOW   ALI PEP POL ARO
                ! adm jr. 8/13/90 acetamide geometry and vibrations
NH2  CC   CT2   50.000    116.50   50.00   2.45000 ! ALLOW   ALI PEP POL ARO
! Modified for CYG residue
!S  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  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  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
! Modified for CYG residue
NH3  CT1  CD      50.000   107.0000 ! ALLOW   PEP POL ARO ALI
                ! new aliphatics, adm jr., 2/3/92
NH3  CT1  CC     43.700   110.0000 ! ALLOW   PEP POL ARO ALI
                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
NH3  CT1  CT1    67.700   110.0000 ! ALLOW   ALI POL
                ! new aliphatics, adm jr., 2/3/92
NH3  CT1  CT2    67.700   110.0000 ! ALLOW   ALI POL
                ! new aliphatics, adm jr., 2/3/92
NH3  CT1  CT3    67.700   110.0000 ! ALLOW   ALI POL
                ! new aliphatics, adm jr., 2/3/92
NH3  CT1  HB     51.500   107.5000 ! ALLOW   ALI POL PEP
                ! new aliphatics, adm jr., 2/3/92
NH3  CT2  C      43.700   110.0000 ! ALLOW   PEP POL ARO ALI
                ! alanine (JCS)
NH3  CT2  CC     43.700   110.0000 ! ALLOW   PEP POL ARO ALI
                ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
NH3  CT2  CD     43.700   110.0000 ! ALLOW   PEP POL ARO ALI
                ! adm jr. 5/02/91, acetic acid pure solvent
NH3  CT2  CT2    67.700   110.0000 ! ALLOW   ALI POL
                ! alanine (JCS)
NH3  CT2  HA    45.000    107.50   35.00   2.10100 ! ALLOW   ALI POL
                ! new stretch and bend; methylammonium (KK 03/10/92)
NH3  CT2  HB     51.500   107.5000 ! ALLOW   ALI POL PEP
                ! for use on NTER -- from NH3 CT2HA (JCS) -- (LK)
NH3  CT3  HA    45.000    107.50   35.00   2.10100 ! ALLOW   ALI POL
                ! new stretch and bend; methylammonium (KK 03/10/92)
NP   CP1  C      50.000   106.0000 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP   CP1  CC     50.000   106.0000 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP   CP1  CD     50.000   106.0000 ! ALLOW PRO PEP
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP   CP1  CP2    70.000   108.5000 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP   CP1  HB     51.500   107.5000 ! ALLOW ALI POL PEP PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP   CP3  CP2    70.000   108.5000 ! ALLOW PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP   CP3  HA     51.500   109.1500 ! ALLOW PEP PRO
                ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NPH  CPA  CPB   122.000   111.5400 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH  CPA  CPM    88.000   124.3900 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH  FE   CM     50.000    90.0000 ! ALLOW HEM
                ! Heme (6-liganded): ligand links (KK 05/13/91)
NPH  FE   CPM     0.000    45.0000 ! ALLOW HEM
                ! Heme (6-liganded): for "ic para" only  (KK 05/13/91)
NPH  FE   NPH    14.390    90.0000 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NR1  CPH1 CPH1  130.000   106.0000 ! ALLOW ARO
                ! his, ADM JR., 7/20/89
NR1  CPH1 CT2    45.800   124.0000 ! ALLOW ARO
                ! his, ADM JR., 7/22/89, FC FROM CA CT2CT
NR1  CPH1 CT3    45.800   124.0000 ! ALLOW ARO
                ! his, ADM JR., 7/22/89, FC FROM CA CT2CT
NR1  CPH1 HR3   25.000    124.00   20.00   2.14000 ! ALLOW ARO
                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
NR1  CPH2 HR1   25.000    122.50   20.00   2.14000 ! ALLOW ARO
                ! his, adm jr., 6/27/90
NR2  CPH1 CPH1  130.000   110.0000 ! ALLOW ARO
                ! his, ADM JR., 7/20/89
NR2  CPH1 CT2    45.800   120.0000 ! ALLOW ARO
                ! his, ADM JR., 7/22/89, FC FROM CA CT2CT
NR2  CPH1 HR3   25.000    120.00   20.00   2.14000 ! ALLOW ARO
                ! adm jr., 3/24/92, maintain old aliphatic H VDW params
NR2  CPH2 HR1   25.000    125.00   20.00   2.12000 ! ALLOW ARO
                ! his, adm jr., 6/27/90
NR2  CPH2 NR1   130.000   112.5000 ! ALLOW ARO
                ! his, adm jr., 6/27/90
NR2  FE   CM     50.000   180.0000 ! ALLOW HEM
                ! Heme (6-liganded): ligand links (KK 05/13/91)
NR2  FE   NPH    50.000    90.0000 ! ALLOW HEM
                ! Heme (6-liganded): ligand links (KK 05/13/91)
NR3  CPH1 CPH1  145.000   108.0000 ! ALLOW ARO
                ! his, ADM JR., 7/20/89
NR3  CPH1 CT2    45.800   122.0000 ! ALLOW ARO
                ! his, ADM JR., 7/22/89, FC FROM CA CT2CT
NR3  CPH1 HR1   22.000    122.00   15.00   2.18000 ! ALLOW ARO
                ! his, adm jr., 6/27/90
NR3  CPH2 HR2   32.000    126.00   25.00   2.14000 ! ALLOW ARO
                ! 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
! Modified for CYG residue
!O    CC   S     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
! Modified for CYG residue
OH1  CD   CT1    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  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
CA   CA   ON2b  75.0     120.0  !phenol phosphate, 6/94, adm jr.
CA   ON2b P     90.0     120.0  20.   2.30 !phenol phosphate, 6/94, adm jr.
ON4  P    ON2b  48.1     108.0  !phenol phosphate, 6/94, adm jr.
ON3  P    ON2b  98.9     103.0  !phenol phosphate, 6/94, adm jr.
!nucleic acid section
!NICH parameters to maintain back compatibility following
!atom type switch from HN3 to HN6
NN2  CN3C HN6     42.0     119.0  !nad/ppi, jjp1/adm jr. 7/95
HN6  CN3C CN3     42.0     119.0  !nadh/ppi, jjp1/adm jr. 7/95
HN6  CN3  CN8     30.0     116.0  !nadh/ppi, jjp1/adm jr. 7/95
CN3C CN3  HN6     42.0     119.0  !nadh/ppi, jjp1/adm jr. 7/95
! pyrmidines
!@@@@@@@@ Adenine
! ade 6-mem ring
CN2  NN3A CN4     90.0     117.8  !6R) adm jr. 11/97
NN3A CN4  NN3A    60.0     133.0  !6R)
CN4  NN3A CN5     90.0     110.1  !6R)
CN5  CN5  NN3A    60.0     127.4  !6R) bridgeC4
CN2  CN5  CN5     60.0     121.0  !6R) bridgeC5
CN5  CN2  NN3A    60.0     110.7  !6R)
CN5  CN5  NN2    100.0     105.7  !5R) bridgeC4
CN5  CN5  NN4    100.0     110.0  !5R) bridgeC5
CN4  NN4  CN5    120.0     104.6  !5R)
NN2  CN4  NN4    100.0     113.4  !5R)
CN4  NN2  CN5    100.0     106.3  !5R)
NN2  CN5  NN3A   100.0     126.9  !bridgeC4
CN2  CN5  NN4    100.0     129.0  !bridgeC5
HN3  CN4  NN3A    38.0     113.5  !h2
NN3A CN2  NN1     50.0     130.7  !n6
CN5  CN2  NN1     50.0     118.6  !
CN2  NN1  HN1     40.0     121.5  !h61,h62, C,A,G
HN1  NN1  HN1     31.0     117.0  !C,A,G
NN4  CN4  HN3     39.0     124.8  !h8, G,A
NN2  CN4  HN3     39.0     121.8  !
CN5  NN2  HN2     30.0     129.4  !h9
CN4  NN2  HN2     30.0     125.0  !
!@@@@@@@@ Guanine
! gua 6-mem ring
CN1  NN2G CN2     70.0     131.1  !6R)G, adm jr. 11/97
NN2G CN2  NN3G    70.0     122.2  !6R)
CN2  NN3G CN5     90.0     109.4  !6R)
CN5G CN5  NN3G    70.0     129.9  !6R) bridgeC4
CN1  CN5G CN5     70.0     119.6  !6R) bridgeC5
CN5G CN1  NN2G    70.0     107.8  !6R)
CN5G CN5  NN2B   100.0     104.6  !5R) bridgeC4
CN5  CN5G NN4    100.0     111.4  !5R) bridgeC5
CN4  NN4  CN5G   120.0     103.8  !5R)
NN2B CN4  NN4    100.0     113.0  !5R)
CN4  NN2B CN5    100.0     107.2  !5R)
NN2B CN5  NN3G   140.0     125.5  ! bridgeC4
CN1  CN5G NN4    125.0     129.0  ! bridgeC5
CN1  NN2G HN2     45.0     113.3  ! h1
CN2  NN2G HN2     45.0     115.6  !
NN1  CN2  NN2G    95.0     115.4  ! n2 
NN1  CN2  NN3G    95.0     122.4  !
NN2G CN1  ON1     50.0     127.5  ! o6
CN5G CN1  ON1     50.0     124.7  !
HN3  CN4  NN2B    40.0     122.2  ! h8 (NN4 CN4 HN3 124.8)
CN4  NN2B HN2     30.0     124.6  ! h9
CN5  NN2B HN2     30.0     129.3  !
!@@@@@@@@ Cytosine
! cyt 6-mem ring
CN1  NN2  CN3     50.0     124.1  !C, adm jr. 11/97
NN2  CN1  NN3     50.0     116.8  !C
CN1  NN3  CN2     85.0     119.1  !C
CN3  CN2  NN3     85.0     119.3  !C
CN2  CN3  CN3     85.0     117.8  !C
CN3  CN3  NN2     85.0     122.9  !C
CN1  NN2  HN2     37.0     121.2  !C, h1
CN3  NN2  HN2     37.0     114.7  !C
NN2  CN1  ON1C   130.0     119.4  !C, o2
NN3  CN1  ON1C   130.0     123.8  !C
NN3  CN2  NN1     81.0     122.3  !C, n4
CN3  CN2  NN1     81.0     118.4  !C
CN2  CN3  HN3     38.0     120.1  !C h5
CN3  CN3  HN3     38.0     122.1  !C,U
HN3  CN3  NN2     44.0     115.0  !C, h6
!@@@@@@@@ Uracil
! ura 6-mem ring
CN1T NN2B CN3     70.0     122.0  !U, adm jr. 11/97
NN2B CN1T NN2U    50.0     114.0  !U
CN1T NN2U CN1     50.0     130.2  !U
NN2U CN1  CN3     70.0     112.6  !U
CN1  CN3  CN3    100.0     117.6  !U
CN3  CN3  NN2B   100.0     123.6  !U
CN1T NN2B HN2     40.5     122.0  !U, h1
CN3  NN2B HN2     32.0     116.0  !U
NN2B CN1T ON1    100.0     121.6  !U, o2
NN2U CN1T ON1    100.0     124.4  !U
CN1T NN2U HN2     40.5     114.4  !U, h3
CN1  NN2U HN2     40.5     115.4  !U
NN2U CN1  ON1    100.0     121.9  !U, o4
CN3  CN1  ON1    100.0     125.5  !U, 
CN1  CN3  HN3     30.0     120.3  !U, h5
HN3  CN3  NN2B    30.0     114.3  !U, h6
! thymine 6-mem ring (unique from ura)
CN3T CN1 NN2U     70.0     113.5  !T, adm jr. 11/97
CN1  CN3T CN3    120.0     116.7  !T
CN3T CN3  NN2B   120.0     123.6  !125.3  !T
CN3T CN1  ON1    100.0     124.6  !T, o4
CN1  CN3T CN9     38.0     118.7  !T, c5 methyl
CN3  CN3T CN9     38.0     124.6  !T
CN3T CN3  HN3     30.0     122.1  !T, h6
! Inosine, adm jr., 9/98 update
HN3  CN4  NN3I    35.0     116.75 !c2
HN3  CN4  NN2G    35.0     115.75 !c2
NN3I CN4  NN2G    80.0     127.5  !c2
CN5G CN5  NN3I   100.0     127.0  !c4, r6
NN2B CN5  NN3I   140.0     128.4  !c4, r5
CN1  NN2G CN4    125.0     129.7  !n1
CN4  NN2G HN2     40.5     117.0  !n1
CN4  NN3I CN5     90.0     108.4  !n3
! base to methyl connection 
CN1T NN2B CN9     70.0     116.0  !1-M-T/U, adm jr. 
CN3  NN2B CN9     70.0     122.0  !1-M-T/U, adm jr. 7/24/91
CN1  NN2  CN9     70.0     115.4  !1-M-C, adm jr. 
CN3  NN2  CN9     70.0     120.5  !1-M-C, adm jr. 7/24/91
CN5  NN2  CN9     70.0     125.9  !9-M-A, adm jr.
CN4  NN2  CN9     70.0     127.8  !9-M-A, adm jr.
CN5  NN2B CN9     70.0     125.9  !9-M-G, adm jr.
CN4  NN2B CN9     70.0     126.9  !9-M-G, adm jr.
CN5  NN2B CN8     70.0     125.9  !9-E-G, adm jr.
CN4  NN2B CN8     70.0     126.9  !9-E-G, adm jr.
NN2B CN8  CN9     70.0     113.7  !9-E-G, adm jr.
!===== For glycosydic linkage, base to c1'
CN1T NN2B CN7B    45.0     118.4  !U/T, FC from A
CN3  NN2B CN7B    45.0     119.6  !U/T
CN1  NN2  CN7B    45.0     120.0  !C, FC from A
CN3  NN2  CN7B    45.0     115.9  !C
CN5  NN2  CN7B    45.0     126.1  !A
CN4  NN2  CN7B    45.0     127.6  !A
CN5  NN2B CN7B    45.0     126.5  !G
CN4  NN2B CN7B    45.0     126.3  !G
ON6  CN7B NN2    110.0     108.0  !C/A DNA
ON6B CN7B NN2    110.0     112.0  !C/A RNA
CN8  CN7B NN2    110.0     113.7  !C/A
CN7B CN7B NN2    110.0     111.0  !C/A, RNA
CN7C CN7B NN2    110.0     111.0  !C/A, Arabinose (NF)
ON6  CN7B NN2B   110.0     108.0  !T/U/G (DNA) FC from A
ON6B CN7B NN2B   110.0     112.0  !T/U/G (RNA) FC from A
CN8  CN7B NN2B   110.0     113.7  !T/U/G 
CN7B CN7B NN2B   110.0     111.0  !T/U/G, RNA 
CN7C CN7B NN2B   110.0     111.0  !T/U/G, Arabinose (NF)
HN7  CN7B NN2     43.0     111.0  !
HN7  CN7B NN2B    43.0     111.0  !From HN7  CN7B NN2
!===== End of glycosydic linkage
! remaining terms ordered based on central atom
CN3  CN1A NN1     85.0     113.0  80.0  2.46 !nad/ppi, jjp1/adm jr. 7/95
CN3  CN1A ON1     85.0     118.5  20.0  2.43 !nad/ppi, jjp1/adm jr. 7/95
NN1  CN1A ON1     85.0     128.5  20.0  2.17 !nad/ppi, jjp1/adm jr. 7/95
CN3D CN2  NN1    110.0     116.4  !5mc, adm jr. 9/9/93
CN3D CN2  NN3     30.0     121.3  !5mc, adm jr. 9/9/93
CN1A CN3  CN3C     5.0     107.8  !nad/ppi, jjp1/adm jr. 7/95
CN1A CN3  CN8    125.0     124.2  !nadh/ppi, jjp1/adm jr. 7/95
CN2  CN3D CN3    100.0     117.8  !5mc, adm jr. 9/9/93
CN2  CN3D CN9     40.0     118.0  !5mc, adm jr. 9/9/93
CN3A CN3  CN1A    40.0     110.2  !nad/ppi, jjp1/adm jr. 7/95
CN3B CN3  CN1A    10.0     131.8  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3A CN3     50.0     118.0  !nad/ppi, jjp1/adm jr. 7/95
CN3A CN3  CN3B    40.0     118.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3  CN8     53.5     108.5  !nadh/ppi, jjp1/adm jr. 7/95
CN3B CN3  CN8     53.5     108.5  !nad/ppi, jjp1/adm jr. 7/95
CN3C CN3  CN8     43.5     128.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3D CN9     40.0     124.2  !5mc, adm jr. 9/9/93
CN3D CN3  HN3     30.0     122.0  !5mc, adm jr. 9/9/93
CN3B CN3  HN3B    30.0     122.0  !nad/ppi, jjp1/adm jr. 7/95
CN3A CN3  HN3B    30.0     119.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3C HN3     42.0     119.0  !nadh/ppi, jjp1/adm jr. 7/95
CN3C CN3  HN3     42.0     116.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3A HN3B    80.0     121.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3B HN3B    80.0     120.5  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3B NN2    120.0     122.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3C NN2     60.0     122.0  !nadh/ppi, jjp1/adm jr. 7/95
CN3D CN3  NN2    100.0     124.2  !5mc, adm jr. 9/9/93
CN8  CN3  HN3     30.0     116.0  !nadh/ppi, jjp1/adm jr. 7/95
HN3B CN3B NN2     80.0     117.5  !nad/ppi, jjp1/adm jr. 7/95
HN3  CN3C NN2     42.0     119.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN8  CN3    125.0     108.0  !nadh/ppi, jjp1/adm jr. 7/95
CN3  CN8  HN8     55.0     110.10 !nadh/ppi, jjp1/adm jr. 7/95
CN9  CN8  HN8     34.6     110.10  22.53 2.179 ! Alkanes, sacred
HN8  CN8  NN2     33.43    110.1  !FOR 9-M-ADE(THY), ADM
HN8  CN8  ON5     45.9     108.89 !RIBOSE, Adm Jr. MeOH
CN3  CN9  HN9     33.43    110.10  22.53 2.179 ! Alkanes, sacred
CN3T CN9  HN9     33.43    110.10  22.53 2.179 ! Alkanes, sacred
CN3D CN9  HN9     33.43    110.10  22.53 2.179 ! Alkanes, sacred
CN8  CN9  HN9     34.60    110.10  22.53 2.179 ! Alkanes, sacred
HN9  CN9  NN2     33.43    110.1  !FOR 9-M-A(T), adm jr.
HN9  CN9  NN2B    33.43    110.1  !FOR 9-M-G(C), adm jr.
HN8  CN8  NN2B    33.43    110.1  !FOR 9-E-G, adm jr.
HN9  CN9  ON2     60.0     109.5  !DMP, ADM Jr.
CN1A NN1  HN1     35.0     120.0  !nad/ppi, jjp1/adm jr. 7/95
CN3B NN2  CN3B    30.0     120.0  !nad/ppi, jjp1/adm jr. 7/95
CN3C NN2  CN3C    20.0     114.0  !nadh/ppi, jjp1/adm jr. 7/95
CN3B NN2  CN7B    70.0     121.7  !nad/ppi, jjp1/adm jr. 7/95
CN3C NN2  CN7B    70.0     121.7  !nad/ppi, jjp1/adm jr. 7/95
CN3B NN2  HN2     32.0     117.4  !nad/ppi, jjp1/adm jr. 7/95
CN3C NN2  HN2     39.0     123.0  !nad/ppi, jjp1/adm jr. 7/95
HN1  NN5  HN1     39.0     106.0  ! sugar model, adm jr.
CN9  ON2  P       20.0     120.0  35.   2.33 !DMP, ADM Jr.
CN9  ON2  P2      20.0     120.0  35.   2.33 !nad/ppi, jjp1/adm jr. 7/95
P    ON2  P       15.0     140.0 -40.0  2.80 !nad/ppi, jjp1/adm jr. 7/95
P2   ON2  P       15.0     140.0 -40.0  2.80 !nad/ppi, jjp1/adm jr. 7/95
P2   ON2  P2      15.0     140.0 -40.0  2.80 !nad/ppi, jjp1/adm jr. 7/95
HN4  ON4  P       30.0     115.0  40.0  2.35 !MP_1, ADM Jr. 
HN5  ON5  CN8     57.5     106.0  !RIBOSE, Adm Jr. MeOH
HN5  ON5  CN9     57.5     106.0  !RIBOSE, Adm Jr. MeOH
ON2  P    ON2     80.0     104.3  !DMP, ADM Jr.
ON2  P    ON4     48.1     108.0  !MP_1, ADM Jr.
ON3  P    ON4     98.9     108.23 !MP_1, ADM Jr.
ON4  P    ON4     98.9     104.0  !MP_0, ADM Jr.
ON2  P2   ON2     80.0     104.3  !nad/ppi, jjp1/adm jr. 7/95
ON2  P2   ON3     88.9     111.6  !nad/ppi, jjp1/adm jr. 7/95
ON3  P2   ON3    104.0     120.0  !nad/ppi, jjp1/adm jr. 7/95
CN7  CN8  ON5     75.7     110.10 !RIBOSE, adm jr. MeOH
HN9  CN9  HN9     35.500   108.40  5.40 1.802 !alkane update, adm jr. 3/2/92
!@@@@@@@@@ Beginning of endocyclic valence angles for regular DNA @@@@@@@
CN7  ON6  CN7B    110.0    108.0   ! NF, 11/97, C4'O4'C1'
ON6  CN7B CN8      90.0    102.0   ! NF, 11/97, C4'O4'C1' 
CN7B CN8  CN7      80.00   100.0   ! NF, 11/97, C1'C2'C3'
CN8  CN7  CN7      60.00   102.0   8.0   2.561  !NF, 11/97, C2'C3'C4'
CN7  CN7  ON6     100.0    104.0   ! NF, 11/97, C3'C4'O4'
HN7  CN7  ON6      45.2    107.24  ! 
HN7  CN7B ON6      45.2    107.24  ! 
HN7  CN7  CN7      40.0    108.00  !
CN7B CN8  HN8      33.4    110.10  22.53   2.179 ! following terms directly
CN8  CN7B HN7      33.4    110.10  22.53   2.179 ! from alkanes
HN7  CN7  CN8      34.5    110.1   22.53   2.179 ! 
HN8  CN8  CN7      34.53   110.10  22.53   2.179 ! 
HN8  CN8  CN8      34.53   110.10  22.53   2.179 ! 
HN8  CN8  HN8      35.5    109.00   5.40   1.802 ! 
HN7  CN7  HN7      35.5    109.00   5.40   1.802 !
!@@@@@@@@@ End of endocyclic valence angles for regular DNA @@@@@@@

!@@@@@@@@@ Beginning of endocyclic valence angles for regular RNA @@@@@@@
CN7  ON6B CN7B    110.0    115.0   ! From CN7  ON6  CN7B
CN7  CN7  ON6B    100.0    110.0   ! From CN7  CN7  ON6
ON6B CN7B CN7B     90.0    106.0   ! 030998 
CN7B CN7B CN7     110.0     96.0   ! 
CN7B CN7  CN7      60.0    100.0    8.00   2.561  !NF, 11/97, C2'C3'C4'
HN7  CN7  ON6B     45.2    107.24  !
HN7  CN7B ON6B     45.2    107.24  !
CN7B CN7B HN7      33.4    110.10  22.53   2.179 ! following terms directly
HN7  CN7B HN7      35.5    109.00   5.40   1.802 !
!@@@@@@@@@ End of endocyclic valence angles for regular RNA @@@@@@@

!@@@@@@@@@ Beginning of endocyclic valence angles for arabinose @@@@@@@
ON6  CN7B CN7C     90.0    102.0   ! NF, 11/97, C4'O4'C1'
CN7B CN7C CN7      80.00   100.0   ! NF, 11/97, C1'C2'C3'
CN7C CN7  CN7      60.00   102.0    8.00   2.561  !NF, 11/97, C2'C3'C4'
CN7B CN7C HN7      33.4    110.10  22.53   2.179 ! following terms directly
CN7C CN7B HN7      33.4    110.10  22.53   2.179 ! from alkanes
HN7  CN7  CN7C     34.5    110.1   22.53   2.179 !
HN7  CN7C CN7      34.53   110.10  22.53   2.179 !
HN7  CN7C HN7      35.5    109.00   5.40   1.802 !
!@@@@@@@@@ End of endocyclic valence angles for arabinose @@@@@@@

!@@@@@@@@@ Beginning of exocyclic valence angles for regular DNA @@@@@@@
ON6  CN7  CN8B     90.0    108.2  !NF, 11/97, O4'C4'C5'
CN7  CN7  CN8B     45.0    110.0  !NF, 11/97, C3'C4'C5'
CN7  CN8B ON2      70.0    108.4  !NF, 11/97, C4'C5'O5'
CN7  CN7  ON2     115.0    109.7  !NF, 11/97, C4'C3'O3'
CN7B CN7B ON2     115.0    109.7  !NF, 11/97, C4'C3'O3' for NADPH
CN7  CN7B ON2     115.0    109.7  !NF, 11/97, C4'C3'O3' for NADPH
CN8  CN7  ON2     115.0    109.7  !NF, 11/97, C2'C3'O3'
CN8B ON2  P        20.0    120.0   35.00   2.33 !NF, 11/97, C5'O5'P
CN7  ON2  P        20.0    120.0   35.00   2.33 !NF, 11/97, C3'O3'P
CN7B ON2  P        20.0    120.0   35.00   2.33 !NF, 11/97, C3'O3'P, for NADPH
! sugar
HN7  CN7  CN8B     34.5    110.1   22.53   2.179 ! From HN7  CN7  CN8
HN8  CN8B ON2      60.0    109.5  ! From HN7  CN8  ON2
HN5  ON5  CN8B     57.5    106.0  ! From HN5  ON5  CN8
HN8  CN8B HN8      35.5    109.0    5.40   1.802  ! Alkanes, sacred
HN8  CN8B CN7      34.53   110.1   22.53   2.179  ! Alkanes, sacred
HN7  CN7  ON2      60.0    109.5  !DMP, adm jr. from HN7  CN8  ON2
HN7  CN7B ON2      60.0    109.5  !DMP, adm jr. from HN7  CN8  ON2, for NADPH
!===== For 5ter patch:
CN7  CN8B ON5      75.7    110.10 ! From CN7  CN8B  ON5
HN8  CN8B ON5      45.9    108.89 ! From HN7  CN8  ON5
!===== For 3ter patch:
ON5  CN7  CN8      75.7    110.0  ! from CHARMM22
ON5  CN7  CN7      75.7    110.1  ! 
HN7  CN7  ON5      60.0    109.5  ! 
HN5  ON5  CN7      57.5    109.0  ! 
!@@@@@@@@@ End of exocyclic valence angles for regular DNA @@@@@@@

!@@@@@@@@@ Beginning of exocyclic valence angles for regular RNA @@@@@@@
!O4'-C4'-C5'
ON6B CN7  CN8B     90.0    108.2  ! 
!O3'-C3'-C2'
ON2  CN7  CN7B     90.0    110.0  !
ON5  CN7  CN7B     90.0    110.0  ! From ON5  CN7  CN8
!O2'-C2'-C1'
ON5  CN7B CN7B     80.0    108.4  ! 
!O2'-C2'-C3'
ON5  CN7B CN7      90.0    108.0  ! 
HN7  CN7B ON5      60.0    109.5  !
HN5  ON5  CN7B     57.5    109.0  !
HN7  CN7B CN7      34.53   110.10  22.53   2.179
HN7  CN7  CN7B     34.53   110.10  22.53   2.179

!@@@@@@@@@ End of exocyclic valence angles for regular RNA @@@@@@@

CN7C CN7  ON2     115.0    109.7  !NF, 11/97, C2'C3'O3'
!===== For 3ter patch:
!From DNA:
ON5  CN7  CN7C     75.7    110.0  ! from CHARMM22
!From RNA:
ON5  CN7C CN7B     80.0    108.4  ! From ON5  CN7B CN7B 
!O2'-C2'-C3'
ON5  CN7C CN7      90.0    108.0  ! From ON5  CN7B CN7
HN7  CN7C ON5      60.0    109.5  !
HN5  ON5  CN7C     57.5    109.0  ! 032598

!@@@@@@@@@ Beginning of exocyclic valence angles for arabinose @@@@@@@
!@@@@@@@@@ End of exocyclic valence angles for arabinose @@@@@@@

!@@@@@@@@@ Beginning of angles for the nucleotide analogue @@@@@@@
CN8  ON2  P        20.0    120.0  35.   2.33 !DMP, adm jr.
!@@@@@@@@@ End of angles for the nucleotide analogue @@@@@@@
ON2  P    ON3      98.9    111.6  !DMP, adm jr.
ON3  P    ON3     120.0    120.0  !DMP, adm jr.
HN8  CN8  ON2      60.0    109.5  !DMP, adm jr.
ON5  P    ON3      98.9    111.6  ! From ON2 P ON3
!-- For imidazole, from imidazole alone:
!-- and for link between sugar and imidazole
ON6  CN7B NR1     140.0    108.00  ! k guessed, theta from ribo./desox. xtal (NF)
ON6B CN7B NR1     140.0    108.00  ! RNUS
CN8  CN7B NR1     140.0    113.70  ! k guessed, theta from ribo./desox. xtal (NF)
CN7B CN7B NR1     140.0    113.70  ! RNUS
CN7B NR1  CPH2    130.0    127.00  ! k guessed, theta from A/G xtal (NF)
CN7B NR1  CPH1    130.0    126.00  ! k guessed, theta from A/G xtal (NF)
HN7  CN7B NR1      30.0    106.3  ! k guessed, theta from ai (NF)
!CPH2 NR1  CPH1    130.0    107.0000 ! From imidazole (NF), modified for 360 deg. condition
!CPH2 NR2  CPH1    130.0    104.0000 ! From imidazole (NF)
!NR1  CPH1 CPH1    130.0    106.0000 ! From imidazole (NF)
!NR1  CPH2 NR2     130.0    112.5000 ! From imidazole
!NR2  CPH1 CPH1    130.0    110.0000 ! From imidazole (NF)
!NR1  CPH2 HR1      25.0    122.50   20.00   2.14000 ! From imidazole (NF)
!NR2  CPH2 HR1      25.0    125.00   20.00   2.12000 ! From imidazole (NF)
!HR3  CPH1 CPH1     25.0    130.00   20.00   2.20000 ! From imidazole (NF)
!NR1  CPH1 HR3      25.0    124.00   20.00   2.14000 ! From imidazole (NF)
!NR2  CPH1 HR3      25.0    120.00   20.00   2.14000 ! From imidazole (NF)
!------------------------ For water -------------------
!HT   OT   HT       55.0    104.52 		! FROM TIPS3P GEOMETRY
!------------------------ added for arao -----------------------
!------------------------ added for araim ----------------------
ON6  CN7B CN7     120.0     106.25   ! 
CN7B CN7  CN8      58.35    113.6   11.16 2.561 ! 

DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types             Kchi    n   delta
!
! from lipids
! FROM CHARMM23 Guessed parameters
! Rommie Jerome
! C6-C7
O    CC   CPH1 CPH1      .550    1 180.0 ! param
O    CC   CPH1 NR2     .550    1 0.0 ! param
NH2  CC   CPH1 CPH1      .550    1 0.0 ! param
NH2  CC   CPH1 NR2      .550    1 180.0 ! param
O    CC   CPH1 CPH1	1.7	2 180.0 ! param
!
CC   CPH1 CPH1 NR1      5.200    2 0.0 !cycle
CC   CPH1 CPH1 NC2      5.200    2 0.0 !cycle
NR2  CPH1 CPH1 NC2       5.200    2 0.0 !cycle
CC   CPH1 NR2  CPH2      5.200    2 0.0 !cycle
CPH1 CC   NH2  H      0.200    2 0.0 !  cis or trans terminal NH2
! C8-N4
CPH1 CPH1 NC2  C      1.300    2 180.0 ! param
NR1  CPH1 NC2  C       1.300    2 180.0 ! param
!
CPH2 NR1  CPH1 NC2      0.200    3 0.0 ! cycle
CN7B NR1  CPH1 NC2      0.200    3 0.0 ! cycle
!
CN7B ON6B CN7  CTL3      0.200    3 0.0 !cycle cycle
CN7B CN7  CN7  CTL3      0.200    3 0.!cycle 0
!C4-C9 
*  CN7  CTL3  *      0.200    3 0.0
ON6B CN7  CTL3 OSL      4.00    1 180.0
CN7  CN7  CTL3 OSL      0.200  3 0.0
CN7  CN7  CTL3 HAL3      0.200    3 0.0 
ON6B CN7  CTL3 HAL3      0.200    3 0.0
ON5  CN7  CN7  CTL3      0.200    3 0.0 !cycle
CTL3 CN7  CN7  HN7      0.200    3 0.0 !cycle
OSL  CTL3 CN7  HN7      0.000    3 0.0
HN7  CTL3  CN7  HAL3    0.000    3 0.0
HN7  CN7  CTL3  HAL3   0.200	3 0.0
!C11-C12
NC2  CT2  C    CT2      1.500    1 0.0
NC2  CT2  C    CT2      2.000    2 0.0
NC2  CT2  C    O        0.000    3 0.0
CT2  C    CT2  HA        0.000    3 0.0
!C12-C13
CT2  C    CT2  CT2      1.000    3 0.0
CT2  C    CT2  OH1        0.000    3 0.0
 O    C    CT2  OH1       0.000    3 0.0
!C14-C15
CT2  CT2  CTL3 OSL      0.200    3 0.0
CT2  CT2  CTL3 HAL3      0.200    3 0.0
OH1  CT2  CTL3 OSL      0.200    3 0.0
OH1  CT2  CTL3 HAL3      0.200    3 0.0
OSL  CTL3 CT2  HA       0.200    3 0.0
HA   CT2  CTL3 HAL3      0.200    3 0.0


! END OF CHARMM-GUESSED PARAMETERS


!lipids section
X    CTL1 OHL  X        0.14    3     0.00 ! glycerol
X    CTL2 OHL  X        0.14    3     0.00 ! glycerol
X    CTL3 OHL  X        0.14    3     0.00 ! glycerol
OBL  CL   CTL2 HAL2     0.00    6   180.00 ! acetic acid
OBL  CL   CTL3 HAL3     0.00    6   180.00 ! acetic acid
OSL  CL   CTL2 HAL2     0.00    6   180.00 ! acetic acid
OSL  CL   CTL3 HAL3     0.00    6   180.00 ! acetic acid
OBL  CL   OSL  CTL1     0.965   1   180.00 ! methyl acetate
OBL  CL   OSL  CTL1     3.85    2   180.00 ! methyl acetate
OBL  CL   OSL  CTL2     0.965   1   180.00 ! methyl acetate
OBL  CL   OSL  CTL2     3.85    2   180.00 ! methyl acetate
OBL  CL   OSL  CTL3     0.965   1   180.00 ! methyl acetate
OBL  CL   OSL  CTL3     3.85    2   180.00 ! methyl acetate
X    CL   OSL  X        2.05    2   180.00 ! methyl acetate
X    CTL2 CL   X        0.05    6   180.00 ! methyl acetate
X    CTL3 CL   X        0.05    6   180.00 ! methyl acetate
X    CL   OHL  X        2.05    2   180.00 ! acetic acid
HAL2 CTL2 CL   OHL      0.00    6   180.00
HAL3 CTL3 CL   OHL      0.00    6   180.00
OSL  PL   OSL  CTL2     1.20    1   180.00 ! phosphate, new NA, 4/98, adm jr.
OSL  PL   OSL  CTL2     0.10    2   180.00 ! phosphate, new NA, 4/98, adm jr.
OSL  PL   OSL  CTL2     0.10    3   180.00 ! phosphate, new NA, 4/98, adm jr.
O2L  PL   OSL  CTL2     0.10    3     0.00 ! phosphate, new NA, 4/98, adm jr.
OSL  PL   OSL  CTL3     1.20    1   180.00 ! phosphate, new NA, 4/98, adm jr.
OSL  PL   OSL  CTL3     0.10    2   180.00 ! phosphate, new NA, 4/98, adm jr.
OSL  PL   OSL  CTL3     0.10    3   180.00 ! phosphate, new NA, 4/98, adm jr.
O2L  PL   OSL  CTL3     0.10    3     0.00 ! phosphate, new NA, 4/98, adm jr.
OHL  PL   OSL  CTL2     0.95    2     0.00 ! terminal phosphate
OHL  PL   OSL  CTL2     0.50    3     0.00 ! terminal phosphate
OHL  PL   OSL  CTL3     0.95    2     0.00 ! terminal phosphate
OHL  PL   OSL  CTL3     0.50    3     0.00 ! terminal phosphate
X    OHL  PL   X        0.30    3     0.00 ! terminal phosphate
X    CTL1 OSL  X        0.00    3     0.00 ! phosphate, new NA, 4/98, adm jr.
X    CTL2 OSL  X        0.00    3     0.00 ! phosphate, new NA, 4/98, adm jr.
X    CTL3 OSL  X        0.00    3     0.00 ! phosphate, new NA, 4/98, adm jr.
CTL3 CTL2 OSL  CL       0.7     1   180.00 ! ethyl acetate, 12/92
CTL2 CTL2 OSL  CL       0.7     1   180.00 ! ethyl acetate, 12/92
CTL3 CTL1 OSL  CL       0.7     1   180.00 ! ethyl acetate, 12/92
CTL2 CTL1 OSL  CL       0.7     1   180.00 ! ethyl acetate, 12/92
CTL1 CTL2 CL   OSL     -0.15    1   180.00 ! methyl propionate, 12/92
CTL1 CTL2 CL   OSL      0.53    2   180.00 ! methyl propionate, 12/92
CTL2 CTL2 CL   OSL     -0.15    1   180.00 ! methyl propionate, 12/92
CTL2 CTL2 CL   OSL      0.53    2   180.00 ! methyl propionate, 12/92
CTL3 CTL2 CL   OSL     -0.15    1   180.00 ! methyl propionate, 12/92
CTL3 CTL2 CL   OSL      0.53    2   180.00 ! methyl propionate, 12/92
X    CTL2 NTL  X        0.26    3     0.00 ! tetramethylammonium  
X    CTL5 NTL  X        0.23    3     0.00 ! tetramethylammonium
X    CTL2 NH3L X        0.10    3     0.00 ! ethanolamine
NH3L CTL2 CTL2 OHL      0.7     1   180.00 ! ethanolamine
NH3L CTL2 CTL2 OSL      0.7     1   180.00 ! ethanolamine
NTL  CTL2 CTL2 OHL      4.3     1   180.00 ! choline, 12/92
NTL  CTL2 CTL2 OHL     -0.4     3   180.00 ! choline, 12/92
NTL  CTL2 CTL2 OSL      3.3     1   180.00 ! choline, 12/92
NTL  CTL2 CTL2 OSL     -0.4     3   180.00 ! choline, 12/92
X    CTL1 CTL1 X        0.200   3     0.00 ! alkane, 3/92
X    CTL1 CTL2 X        0.200   3     0.00 ! alkane, 3/92
X    CTL1 CTL3 X        0.200   3     0.00 ! alkane, 3/92
X    CTL2 CTL2 X        0.1900  3     0.00 ! alkane, 4/98, yin and mackerell
X    CTL2 CTL3 X        0.1600  3     0.00 ! alkane, 4/98, yin and mackerell
X    CTL3 CTL3 X        0.1525  3     0.00 ! alkane, 4/98, yin and mackerell
CTL3 CTL2 CTL2 CTL3     0.10    2   180.00 ! alkane, 4/98, adm jr., lower butane gauche conformer
CTL3 CTL2 CTL2 CTL3     0.15    4     0.00 ! alkane, 4/98, adm jr.
CTL3 CTL2 CTL2 CTL3     0.10    6   180.00 ! alkane, 4/98, adm jr.
CTL2 CTL2 CTL2 CTL3     0.10    2   180.00 ! alkane, 4/98, adm jr.
CTL2 CTL2 CTL2 CTL3     0.15    4     0.00 ! alkane, 4/98, adm jr.
CTL2 CTL2 CTL2 CTL3     0.10    6   180.00 ! alkane, 4/98, adm jr.
CTL2 CTL2 CTL2 CTL2     0.10    2   180.00 ! alkane, 4/98, adm jr.
CTL2 CTL2 CTL2 CTL2     0.15    4     0.00 ! alkane, 4/98, adm jr.
CTL2 CTL2 CTL2 CTL2     0.10    6   180.00 ! alkane, 4/98, adm jr.
HAL3 CTL3 OSL  SL       0.00    3     0.00 ! methylsulfate
CTL2 OSL  SL   O2L      0.00    3     0.00 ! methylsulfate
CTL3 OSL  SL   O2L      0.00    3     0.00 ! methylsulfate
HEL1 CEL1 CEL1 HEL1     1.0000  2   180.00 ! 2-butene, adm jr., 8/98 update
CTL3 CEL1 CEL1 HEL1     1.0000  2   180.00 ! 2-butene, adm jr., 8/98 update
X    CEL1 CEL1 X        0.1300  1   180.00 ! 2-butene, adm jr., 8/98 update
X    CEL1 CEL1 X       24.0000  2   180.00 ! 2-butene, adm jr., 8/98 update
X    CEL2 CEL2 X        4.9000  2   180.00 ! ethene, yin,adm jr., 12/95
CTL2 CEL1 CEL2 HEL2     5.2000  2   180.00 ! propene, yin,adm jr., 12/95
CTL3 CEL1 CEL2 HEL2     5.2000  2   180.00 ! propene, yin,adm jr., 12/95
HEL1 CEL1 CEL2 HEL2     5.2000  2   180.00 ! propene, yin,adm jr., 12/95
CEL1 CEL1 CTL2 HAL2     0.0300  3     0.00 ! butene, yin,adm jr., 12/95
CEL1 CEL1 CTL3 HAL3     0.0300  3     0.00 ! butene, yin,adm jr., 12/95
CEL1 CEL1 CTL2 CTL2     0.4000  3     0.00 ! 1-butene, adm jr., 8/98 update
CEL2 CEL1 CTL2 CTL2     0.4000  3     0.00 ! 1-butene, adm jr., 8/98 update
CEL2 CEL1 CTL2 CTL3     0.4000  3     0.00 ! 1-butene, adm jr., 8/98 update
CEL2 CEL1 CTL2 HAL2     0.1200  3     0.00 ! 1-butene, yin,adm jr., 12/95
CEL2 CEL1 CTL3 HAL3     0.050   3   180.00 ! propene, yin,adm jr., 12/95
HEL1 CEL1 CTL2 CTL2     0.1200  3     0.00 ! butene, yin,adm jr., 12/95
HEL1 CEL1 CTL2 CTL3     0.1200  3     0.00 ! butene, yin,adm jr., 12/95
HEL1 CEL1 CTL2 HAL2     0.8700  3     0.00 ! butene, yin,adm jr., 12/95
HEL1 CEL1 CTL3 HAL3     0.3400  3     0.00 ! butene, yin,adm jr., 12/95


!
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  3     0.00 ! 
		! for butene, yin/adm jr., 12/95
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
! Modified for CYG residue
CC  S    CT2  CT1      0.2400  1   180.00 ! ALOW    ALI SUL ION
                ! expt. MeEtS,      3/26/92 (FL)
CC  S    CT2  CT1      0.3700  3     0.00 ! ALOW    ALI SUL ION
                ! expt. MeEtS,      3/26/92 (FL)
!!!!!
                ! 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
! Modified for CYG residue
HA   CT2  S    CC      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  CE2  HE2      5.2000  2   180.00 ! 
		! for propene, yin/adm jr., 12/95
HE1  CE1  CT2  HA       0.8700  3     0.00 ! 
		! for butene, yin/adm jr., 12/95
HE1  CE1  CT2  CT3      0.1200  3     0.00 ! 
		! for butene, yin/adm jr., 12/95
HE1  CE1  CT3  HA       0.3400  3     0.00 ! 
		! for butene, yin/adm jr., 12/95
HE2  CE2  CE1  CT2      5.2000  2   180.00 ! 
		! for 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  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        5.2000  2   180.00 ! 
		! for butene, yin/adm jr., 12/95
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  C    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   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)
! Modified for CYG residue  !!!!!!! should be checked. 
CT2   S   CC  CT2       2.05    2   180.00 ! methyl acetate 
CT2   S   CC  O       2.05    2   180.00 ! methyl acetate 
!
! Modified for CYG residue
CD  OB  OH1 CT1       100.00    0     0.00 ! acetic acid

CA   CA   CA   ON2b      3.10    2   180.0  !phenol phosphate, 6/94, adm jr.
HP   CA   CA   ON2b      4.20    2   180.0  !phenol phosphate, 6/94, adm jr.
CA   CA   ON2b P         1.40    2   180.0  !phenol phosphate, 6/94, adm jr.
CA   CA   ON2b P         0.20    3   180.0  !phenol phosphate, 6/94, adm jr.
CA   ON2b P    ON4       0.95    2     0.0  !phenol phosphate, 6/94, adm jr.
CA   ON2b P    ON4       0.50    3     0.0  !phenol phosphate, 6/94, adm jr.
CA   ON2b P    ON3       0.10    3     0.0  !phenol phosphate, 6/94, adm jr.
!nucleic acid section
! PHOSPHATE
ON2  P    ON2  CN7      1.20    1   180.0  !10/97, DMP, adm jr.
ON2  P    ON2  CN7      0.10    2   180.0  !10/97, DMP, adm jr.
ON2  P    ON2  CN7      0.10    3   180.0  !10/97, DMP, adm jr.
ON2  P    ON2  CN7      0.00    6     0.0  !10/97, DMP, adm jr.
ON2  P    ON2  CN8      1.20    1   180.0  !10/97, DMP, adm jr.
ON2  P    ON2  CN8      0.10    2   180.0  !10/97, DMP, adm jr.
ON2  P    ON2  CN8      0.10    3   180.0  !10/97, DMP, adm jr.
ON2  P    ON2  CN8      0.00    6     0.0  !10/97, DMP, adm jr.
! Added when C5' defined as CN8B (NF 041497):
ON2  P    ON2  CN8B     1.20    1   180.0  !10/97, DMP, adm jr.
ON2  P    ON2  CN8B     0.10    2   180.0  !10/97, DMP, adm jr.
ON2  P    ON2  CN8B     0.10    3   180.0  !10/97, DMP, adm jr.
ON2  P    ON2  CN8B     0.00    6     0.0  !10/97, DMP, adm jr.
ON2  P    ON2  CN9      1.20    1   180.0  !dmp
ON2  P    ON2  CN9      0.10    2   180.0  !dmp
ON2  P    ON2  CN9      0.10    3   180.0  !dmp
ON2  P    ON2  CN9      0.00    6     0.0  !dmp
!
ON3  P    ON2  CN7      0.10    3     0.0  !dmp,eps, O1P-P-O3'-C3'
ON3  P    ON2  CN7B     0.10    3     0.0  !for NADPH
ON3  P    ON2  CN8      0.10    3     0.0  !dmp
ON3  P    ON2  CN8B     0.10    3     0.0  !dmp,bet, O1P-P-O5'-C5'
ON3  P    ON2  CN9      0.10    3     0.0  !dmp
! terminal phosphate terms, adm jr.
ON4  P    ON2  CN7      0.95    2     0.0  !MP_1, adm jr.
ON4  P    ON2  CN7      0.50    3     0.0  !MP_1, adm jr.
ON4  P    ON2  CN7B     0.95    2     0.0  !for NADPH
ON4  P    ON2  CN7B     0.50    3     0.0  !for NADPH
ON4  P    ON2  CN8      0.95    2     0.0  !MP_1, adm jr.
ON4  P    ON2  CN8      0.50    3     0.0  !MP_1, adm jr.
ON4  P    ON2  CN8B     0.95    2     0.0  !MP_1, adm jr.
ON4  P    ON2  CN8B     0.50    3     0.0  !MP_1, adm jr.
ON4  P    ON2  CN9      0.95    2     0.0  !MP_1, adm jr.
ON4  P    ON2  CN9      0.50    3     0.0  !MP_1, adm jr.
X    ON4  P    X        0.30    3     0.0  !MP_1, adm jr.
! When O5' is ON2 (phosphodiester linkage):
P    ON2  CN7  HN7      0.000   3     0.0  !dmp,eps, H-C3'-O3'-P
P    ON2  CN7B HN7      0.000   3     0.0  !for NADPH
P    ON2  CN8B HN8      0.000   3     0.0  !dmp,beta, H-C5'-O5'-P
P    ON2  CN8  HN8      0.000   3     0.0  !dmp
P    ON2  CN9  HN9      0.000   3     0.0  !dmp
! butane gauche terms
cn9  cn8  cn8  cn9      0.15    1     0.0
cn9  cn8  cn8  cn8      0.15    1     0.0
! BASES                     
! Uracil 
NN2B CN1T NN2U CN1      1.5     2   180.0  ! adm jr. 11/97
CN1T NN2U CN1  CN3      1.5     2   180.0  ! adm jr. 11/97
NN2U CN1  CN3  CN3      1.5     2   180.0  ! adm jr. 11/97
CN1  CN3  CN3  NN2B     6.0     2   180.0  ! adm jr. 11/97 
CN3  CN3  NN2B CN1T     1.5     2   180.0  ! adm jr. 11/97
CN3  NN2B CN1T NN2U     1.5     2   180.0  ! adm jr. 11/97
HN3  CN3  CN3  HN3      3.0     2   180.0  ! adm jr. 11/97
HN3  CN3  CN1  ON1      6.0     2   180.0  ! adm jr. 11/97
ON1  CN1T NN2B HN2      0.0     2   180.0  ! adm jr. 11/97
ON1  CN1  NN2U HN2      0.0     2   180.0  ! adm jr. 11/97
ON1  CN1T NN2U HN2      0.0     2   180.0  ! adm jr. 11/97
HN2  NN2B CN3  HN3      1.5     2   180.0  ! adm jr. 11/97
NN2B CN1T NN2U HN2      3.8     2   180.0  ! adm jr. 11/97
CN3  CN1  NN2U HN2      3.8     2   180.0  ! adm jr. 11/97
CN3  CN3  NN2B HN2      1.6     2   180.0  ! adm jr. 11/97
NN2U CN1T NN2B HN2      1.6     2   180.0  ! adm jr. 11/97
!Thymine
CN1T NN2B CN3  CN3T     1.8     2   180.0  ! adm jr. 11/97
NN2U CN1  CN3T CN3      1.8     2   180.0  ! adm jr. 11/97
CN1  CN3T CN3  NN2B     3.0     2   180.0  ! adm jr. 11/97
NN2B CN1  CN3T CN9      5.6     2   180.0  ! adm jr. 11/97
NN2B CN3  CN3T CN9      5.6     2   180.0  ! adm jr. 11/97
CN1  CN3T CN9  HN9      0.46    3     0.0  ! adm jr. 11/97
CN3  CN3T CN9  HN9      0.46    3     0.0  ! adm jr. 11/97
CN3T CN1  NN2U HN2      4.8     2   180.0  ! adm jr. 11/97
! Cytosine 
CN3  NN2  CN1  NN3      0.6     2   180.0  ! adm jr. 11/97
NN2  CN1  NN3  CN2      0.6     2   180.0  ! adm jr. 11/97
CN1  NN3  CN2  CN3      6.0     2   180.0  ! adm jr. 11/97
NN3  CN2  CN3  CN3      0.6     2   180.0  ! adm jr. 11/97
CN2  CN3  CN3  NN2      6.0     2   180.0  ! adm jr. 11/97
CN3  CN3  NN2  CN1      0.6     2   180.0  ! adm jr. 11/97
NN3  CN2  NN1  HN1      1.0     2   180.0  ! adm jr. 11/97
CN3  CN2  NN1  HN1      1.0     2   180.0  ! adm jr. 11/97
NN1  CN2  NN3  CN1      2.0     2   180.0  ! adm jr. 11/97
NN1  CN2  CN3  CN3      2.0     2   180.0  ! adm jr. 11/97
NN1  CN2  CN3  HN3      2.0     2   180.0  ! adm jr. 11/97
ON1C CN1  NN2  HN2      3.0     2   180.0  ! adm jr. 11/97
ON1C CN1  NN3  CN2      1.6     2   180.0  ! adm jr. 11/97
ON1C CN1  NN2  CN3      1.6     2   180.0  ! adm jr. 11/97
NN3  CN2  CN3  HN3      3.4     2   180.0  ! adm jr. 11/97
NN2  CN3  CN3  HN3      3.4     2   180.0  ! adm jr. 11/97
CN2  CN3  CN3  HN3      4.6     2   180.0  ! adm jr. 11/97
CN1  NN2  CN3  HN3      4.6     2   180.0  ! adm jr. 11/97
X    CN2  NN3  X        2.0     2   180.0  ! adm jr. 11/97
! 5-methylcytosine
NN2  CN3  CN3D CN2      3.0     2   180.0  !5mc, adm jr. 9/9/93
CN3  CN3D CN2  NN3      1.0     2   180.0  !5mc, adm jr. 9/9/93
CN3D CN2  NN3  CN1     10.0     2   180.0  !5mc, adm jr. 9/9/93
CN3D CN3  NN2  CN1      1.0     2   180.0  !5mc, adm jr. 9/9/93
CN3D CN2  NN1  HN1      2.0     2   180.0  !5mc, adm jr. 9/9/93
NN1  CN2  CN3D CN3      0.0     2   180.0  !5mc, adm jr. 9/9/93
NN1  CN2  CN3D CN9      0.0     2   180.0  !5mc, adm jr. 9/9/93
NN2  CN3  CN3D CN9      4.0     2   180.0  !5mc, adm jr. 9/9/93
NN3  CN2  CN3D CN9      0.0     2   180.0  !5mc, adm jr. 9/9/93
CN3  CN3D CN9  HN9      0.0     3     0.0  !5mc, adm jr. 9/9/93
CN2  CN3D CN9  HN9      0.35    3     0.0  !5mc, adm jr. 9/9/93
CN2  CN3D CN3  HN3      4.0     2   180.0  !5mc, adm jr. 9/9/93
CN9  CN3D CN3  HN3      4.0     2   180.0  !5mc, adm jr. 9/9/93
! Adenine  
CN2  NN3A CN4  NN3A     1.8     2   180.0  ! adm jr. 11/97, 6-mem
NN3A CN4  NN3A CN5      2.0     2   180.0  ! 
CN4  NN3A CN5  CN5      1.8     2   180.0  ! 
NN3A CN5  CN5  CN2      2.0     2   180.0  ! treated 2x
CN5  CN5  CN2  NN3A     1.8     2   180.0  ! 
CN5  CN2  NN3A CN4     10.0     2   180.0  ! 
CN5  CN5  NN4  CN4      6.0     2   180.0  ! 5-mem
CN5  NN4  CN4  NN2     14.0     2   180.0  ! 
NN4  CN4  NN2  CN5      6.0     2   180.0  ! 
CN4  NN2  CN5  CN5      6.0     2   180.0  !
NN2  CN5  CN5  NN4     14.0     2   180.0  ! treated 2x
CN2  NN3A CN4  HN3      8.5     2   180.0  ! H2
CN5  NN3A CN4  HN3      8.5     2   180.0  ! H2
CN5  NN4  CN4  HN3      5.2     2   180.0  ! H8
CN5  NN2  CN4  HN3      5.2     2   180.0  ! H8
CN5  CN5  NN2  HN2      1.2     2   180.0  ! H9
NN4  CN4  NN2  HN2      1.2     2   180.0  ! H9
HN2  NN2  CN4  HN3      0.0     2   180.0  ! H8-C-N-H9
CN4  NN3A CN2  NN1      4.0     2   180.0  ! N6
CN5  CN5  CN2  NN1      4.0     2   180.0  ! N6
NN4  CN5  CN2  NN1      0.0     2   180.0  ! N6
CN5  CN2  NN1  HN1      0.5     2   180.0  ! 6-NH2
NN3A CN2  NN1  HN1      0.5     2   180.0  ! 
! Butterfly motion
NN3A CN5  CN5  NN4      7.0     2   180.0  !A, adm jr. 11/97
CN2  CN5  CN5  NN2      7.0     2   180.0  !A
NN3A CN2  CN5  NN4      2.0     2   180.0  !A
CN2  CN5  NN4  CN4      2.0     2   180.0  !A
CN4  NN3A CN5  NN2      2.0     2   180.0  !A
NN3A CN5  NN2  CN4      2.0     2   180.0  !A
! Guanine 
CN1  NN2G CN2  NN3G     0.2     2   180.0  !adm jr. 11/97, 6-mem
NN2G CN2  NN3G CN5      2.0     2   180.0  !
CN2  NN3G CN5  CN5G     0.2     2   180.0  !
NN3G CN5  CN5G CN1      2.0     2   180.0  !
CN5  CN5G CN1  NN2G     0.2     2   180.0  !
CN5G CN1  NN2G CN2      0.2     2   180.0  !
CN5  CN5G NN4  CN4      6.0     2   180.0  !5-mem
CN5G NN4  CN4  NN2B    16.0     2   180.0  !
NN4  CN4  NN2B CN5      6.0     2   180.0  !
CN4  NN2B CN5  CN5G     6.0     2   180.0  !
NN2B CN5  CN5G NN4     10.0     2   180.0  !
! substitutents
ON1  CN1  CN5G CN5     14.0     2   180.0  !G, O6
ON1  CN1  CN5G NN4      0.0     2   180.0  !
ON1  CN1  NN2G CN2     14.0     2   180.0  !
ON1  CN1  NN2G HN2      0.0     2   180.0  !
NN1  CN2  NN2G CN1      4.0     2   180.0  !G, N2
NN1  CN2  NN3G CN5      4.0     2   180.0  !
NN1  CN2  NN2G HN2      0.0     2   180.0  !
NN2G CN2  NN1  HN1      1.2     2   180.0  !
NN3G CN2  NN1  HN1      1.2     2   180.0  !
HN2  NN2G CN1  CN5G     3.6     2   180.0  !G, H1
HN2  NN2G CN2  NN3G     3.6     2   180.0  !
HN3  CN4  NN4  CN5G     5.6     2   180.0  !G, H8
HN3  CN4  NN2B CN5      5.6     2   180.0  !
HN3  CN4  NN2B HN2      0.0     2   180.0  !
HN2  NN2B CN5  CN5G     1.2     2   180.0  !G, H9
HN2  NN2B CN5  NN3G     1.2     2   180.0  !
HN2  NN2B CN4  NN4      1.2     2   180.0  !
! Butterfly motion
NN3G CN5  CN5G NN4     10.0     2   180.0  !adm jr. 11/97
CN1  CN5G CN5  NN2     10.0     2   180.0  !
NN2G CN1  CN5G NN4      2.0     2   180.0  !
CN1  CN5G NN4  CN4      2.0     2   180.0  !
CN2  NN3G CN5  NN2B     2.0     2   180.0  !
NN3G CN5  NN2B CN4      2.0     2   180.0  !
! inosine, adm jr. 2/94
CN5  CN5  NN3I CN4      6.0     2   180.0
NN2G CN4  NN3I CN5      6.0     2   180.0
NN3I CN4  NN2G HN2      1.5     2   180.0
NN3I CN4  NN2G CN1      1.5     2   180.0
HN3  CN4  NN2G HN2      1.5     2   180.0
HN3  CN4  NN2G CN1      1.5     2   180.0
! Wild cards for inosine
X    CN4  NN3I X        3.5     2   180.0
X    CN5  NN3I X        1.0     2   180.0
! Wild cards for uracil, thymine and cytosine
X    CN1  NN3  X        1.0     2   180.0  ! c22
X    CN1  NN2  X        0.9     2   180.0  ! c22
X    CN1T NN2B X        0.9     2   180.0  ! From X CN1 NN2 X, for thymines 
X    CN1  NN2G X        0.9     2   180.0  ! c22
X    CN1  NN2U X        0.9     2   180.0  ! c22
X    CN1T NN2U X        0.9     2   180.0  ! c22
X    CN3  NN2  X        1.0     2   180.0  ! c22
X    CN3  NN2B X        1.0     2   180.0  ! From X CN3 NN2 X, for thymines
X    CN3  CN3  X        1.0     2   180.0  ! c22
X    CN3  CN3T X        1.0     2   180.0  !T, adm jr. 11/97
X    CN1  CN3  X        1.0     2   180.0  ! c22
X    CN1  CN3T X        1.0     2   180.0  !T, adm jr. 11/97
X    CN2  CN3  X        0.8     2   180.0  ! c22
! Wild cards for adenine and guanine
X    CN1  CN5G X        1.0     2   180.0  ! adm jr. 11/97
X    CN2  NN2G X        1.0     2   180.0  ! 
X    CN2  CN5  X        1.0     2   180.0  ! 
X    CN4  NN2  X        1.5     2   180.0  ! 
X    CN4  NN2B X        1.5     2   180.0  ! From X CN4 NN2 X
X    CN4  NN3A X        3.5     2   180.0  ! 
X    CN4  NN4  X        2.0     2   180.0  ! A,G
X    CN5  CN5  X        0.0     2   180.0  !
X    CN5G CN5  X        0.0     2   180.0  ! adm jr. 11/97
X    CN5  NN2  X        1.5     2   180.0  !
X    CN5  NN2B X        1.5     2   180.0  ! From X CN5 NN2 X
X    CN5  NN3A X        1.0     2   180.0  !
X    CN5  NN3G X        1.0     2   180.0  ! adm jr. 11/97
X    CN5  NN4  X        1.0     2   180.0  !
X    CN5G NN4  X        1.0     2   180.0  ! adm jr. 11/97
X    CN2  NN3A X        1.0     2   180.0  !
X    CN2  NN3G X        1.0     2   180.0  ! adm jr. 11/97
! MISC.          
CN1  NN2  CN9  HN9      0.19    3     0.0 ! 1-M-C
CN3  NN2  CN9  HN9      0.00    3     0.0 ! 1-M-C
CN4  NN2  CN9  HN9      0.00    3     0.0 ! 9-M-A
CN5  NN2  CN9  HN9      0.19    3     0.0 ! 9-M-A
CN1  NN2B CN9  HN9      0.19    3     0.0 ! 1-M-U
CN1T NN2B CN9  HN9      0.19    3     0.0 ! 1-M-T
CN3  NN2B CN9  HN9      0.00    3     0.0 ! 1-M-T/U
CN4  NN2B CN9  HN9      0.00    3     0.0 ! 9-M-G
CN5  NN2B CN9  HN9      0.19    3     0.0 ! 9-M-G
CN4  NN2B CN8  HN8      0.00    3     0.0 ! 9-E-G
CN5  NN2B CN8  HN8      0.19    3     0.0 ! 9-E-G
CN4  NN2B CN8  CN9      0.00    3     0.0 ! 9-E-G
CN5  NN2B CN8  CN9      0.19    3     0.0 ! 9-E-G
X    CN8  CN8  X        0.15    3     0.0 ! Alkanes (0.2 to 0.15)
X    CN8  CN9  X        0.15    3     0.0 ! Alkanes (0.2 to 0.15)
! nicotinamide adenine dinucleotide
CN3  NN2  CN3B HN3B     7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
HN2  NN2  CN3B HN3B     3.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
HN3B CN3  CN3A HN3B     2.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
HN3B CN3  CN3B HN3B     1.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
NN2  CN3B CN3  HN3B     7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN1A CN3  HN3B     7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN1A CN3  CN3B HN3B     1.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN1A CN3  CN3A HN3B     5.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN1A CN3  HN3      7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN1A CN3  CN3  HN3      1.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3A CN3  CN1A ON1      2.38    2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3B CN3  CN1A ON1      2.38    2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3A CN3  CN1A NN1      0.35    1   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3A CN3  CN1A NN1      0.62    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
CN3B CN3  CN1A NN1      0.35    1     0.0  !nad/ppi, jjp1/adm jr. 7/95
CN3B CN3  CN1A NN1      0.62    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3A CN3  CN1A     3.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  CN3A CN3  CN3B     6.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
NN2  CN3B CN3  CN3A     7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3B NN2  CN3B CN3      4.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
X    CN3  CN3A X        1.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
X    CN3  CN3B X        1.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
X    CN3  CN8  X        1.0     3   180.0  !nad/ppi, jjp1/adm jr. 7/95
X    NN1  CN1A X        2.5     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
X    NN2  CN3B X        1.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
! nicotinamide adenine dinucleotide hydride, nadh
CN8  CN3  CN1A ON1      1.00    2   180.0  !nadh, jjp1,adm jr. 4/95
CN8  CN3  CN1A ON1      1.00    3     0.0  !nadh, jjp1,adm jr. 4/95
CN8  CN3  CN1A ON1      0.40    6     0.0  !nadh, jjp1,adm jr. 4/95
CN8  CN3  CN1A NN1      0.50    2   180.0  !nadh, jjp1,adm jr. 4/95
CN8  CN3  CN1A NN1      0.35    3   180.0  !nadh, jjp1,adm jr. 4/95
CN8  CN3  CN1A NN1      0.40    6     0.0  !nadh, jjp1,adm jr. 4/95
CN3C CN3  CN1A ON1      0.30    1     0.0  !nadh, jjp1,adm jr. 4/95
CN3C CN3  CN1A ON1      1.95    2   180.0  !nadh, jjp1,adm jr. 4/95
CN3C CN3  CN1A NN1      1.10    1   180.0  !nadh, jjp1,adm jr. 4/95
CN3C CN3  CN1A NN1      1.95    2   180.0  !nadh, jjp1,adm jr. 4/95
HN2  NN2  CN3C HN3      4.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3  NN2  CN3C HN3      7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
NN2  CN3C CN3  HN3      7.0     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN8  CN3  CN3C NN2      0.1     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3C CN3  CN8  CN3      4.0     3   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN1A CN3  CN3C NN2      2.5     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
X    CN3  CN3C X        0.1     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
X    NN2  CN3C X        0.1     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
CN3C NN2  CN3C CN3      0.1     2   180.0  !nad/ppi, jjp1/adm jr. 7/95
! pyrophosphate (ppi)
P2   ON2  P    ON2      0.03    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
P2   ON2  P    ON2      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
P    ON2  P2   ON2      0.03    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
P    ON2  P2   ON2      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
P2   ON2  P2   ON2      0.03    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
P2   ON2  P2   ON2      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
P    ON2  P    ON2      0.03    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
P    ON2  P    ON2      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
P    ON2  P    ON3      0.10    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
P    ON2  P    ON3      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
P    ON2  P2   ON3      0.10    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
P    ON2  P2   ON3      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
P2   ON2  P    ON3      0.10    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
P2   ON2  P    ON3      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
P2   ON2  P2   ON3      0.10    2     0.0  !nad/ppi, jjp1/adm jr. 7/95
P2   ON2  P2   ON3      0.03    3     0.0  !nad/ppi, jjp1/adm jr. 7/95
!for nadp/nadph, adm jr.
HN7  CN7  CN7B ON5       0.195   3         0.0
HN7  CN7  CN7  CN7       0.195   3         0.0
HN7  CN7  CN7  CN7B      0.195   3         0.0
HN7  CN7B CN7  CN7       0.195   3         0.0
HN7  CN7B NN2  CN3B      0.195   3         0.0
HN7  CN7B NN2  CN3C      0.195   3         0.0
HN7  CN7  CN7B HN7       0.195   3         0.0
HN7  CN7  CN7B ON6       0.195   3         0.0
HN7  CN7  CN7B ON2       0.195   3         0.0
HN7  CN7B CN7B ON2       0.195   3         0.0
HN7  CN7  CN7B NN2       0.195   3         0.0

! it conflicts with a term transfered from rna to dna:
!CN7B CN7  ON5  HN5       0.0     3         0.0
!ON5  CN7  CN7B HN7       0.195   3         0.0
!HN7  CN7B CN7  ON2       0.195   3         0.0
!P    ON2  CN7  CN7B      0.0     3         0.0

ON6  CN7B CN7  ON5       3.4     1       180.0 !gam
CN7  CN7B NN2  CN3B      0.0     3         0.0
CN7B CN7B NN2  CN3B      0.0     3         0.0 ! for NADPH
ON6  CN7B NN2  CN3B      0.0     3         0.0 !
ON6B CN7B NN2  CN3B      0.0     3         0.0 ! for NADPH
CN7  CN7B NN2  CN3C      0.0     3         0.0
CN7B CN7B NN2  CN3C      0.0     3         0.0 ! for NADPH
ON6  CN7B NN2  CN3C      0.0     3         0.0 !
ON6B CN7B NN2  CN3C      0.0     3         0.0 ! for NADPH
CN7  CN7  CN7B NN2       0.0     3         0.0
CN7  CN7B NN2  CN5       0.3     3         0.0 ! NF
CN7  CN7B NN2  CN4       0.0     3       180.0 ! NF
ON2  CN7  CN7B NN2       0.0     3         0.0
ON2  CN7B CN7B NN2       0.0     3         0.0 !for NADPH
ON5  CN7  CN7B NN2       0.0     3         0.0

! sugar, replace with ribose terms 021998
CN7  CN7B ON6  CN7       0.6     6       180.0 
CN7B CN7  CN7  CN7       0.4     6         0.0 ! good for amplitudes
CN7  CN7  CN7  ON6       0.6     6         0.0
CN7  CN7  CN7B ON6       0.6     6         0.0
ON2  CN7  CN7  CN7       0.8     6         0.0 !
ON2  CN7  CN7  CN7       0.4     5         0.0 ! Moves the barrier right
ON2  CN7  CN7  CN7       2.0     3       180.0 !
! for ndph
ON2  CN7B CN7  CN7       0.8     6         0.0 !
ON2  CN7B CN7  CN7       0.4     5         0.0 ! Moves the barrier right
ON2  CN7B CN7  CN7       2.0     3       180.0 !
!
ON5  CN7  CN7  CN7       0.8     6         0.0 !
ON5  CN7  CN7  CN7       0.4     5         0.0 ! Moves the barrier right
ON5  CN7  CN7  CN7       2.0     3       180.0 !
ON5  CN7  CN7  ON5       0.0     3         0.0 ! 
ON5  CN7  CN7  ON2       0.0     3         0.0 ! 
ON2  CN7  CN7B ON6       0.5     6         0.0 !good for amplitudes
ON2  CN7  CN7B ON6       0.3     5         0.0 !impact on amplitudes
ON2  CN7  CN7B ON6       0.6     4       180.0 !increases c2'endo
ON2  CN7  CN7B ON6       0.2     3         0.0 !
CN7  CN7  CN7  CN8B      0.5     4       180.0 !del lowers 180 deg.

!============ new parameters for sugar model compounds ===============
!---------------- added for thf-imidazole ------------------
!-- For link between base and sugar:
CN7B NR1  CPH1 HR3      0.0     2   180.0  !NF
CN7B NR1  CPH1 CPH1     0.0     1     0.0  !
CN7B NR1  CPH2 HR1      0.0     2   180.0  !
CN7B NR1  CPH2 NR2      0.0     2   180.0  !
!-- For chi:
ON6  CN7B NR1  CPH1     0.2     3     0.0  ! 
!ON6  CN7B NR1  CPH1     0.5     2   -70.0  !
ON6  CN7B NR1  CPH1     0.5     2   000.0  ! phase changed from above Jerome
ON6  CN7B NR1  CPH1     0.6     1   180.0  !
ON6  CN7B NR1  CPH2     0.3     1     0.0  !

ON6B CN7B NR1  CPH1     0.2     3     0.0  ! RNUS
!ON6B CN7B NR1  CPH1     0.5     2   -70.0  ! RNUS
ON6B CN7B NR1  CPH1     0.5     2   000.0  ! RNUS ! phase changed from above Jerome
ON6B CN7B NR1  CPH1     0.6     1   180.0  ! RNUS
ON6B CN7B NR1  CPH2     0.3     1     0.0  ! RNUS

CN8  CN7B NR1  CPH1     0.2     4     0.0  ! 
CN8  CN7B NR1  CPH2     0.1     3   180.0  !
CN8  CN7B NR1  CPH2     0.3     2     0.0  !
CN8  CN7B NR1  CPH2     0.0     1   180.0  !

CN7B CN7B NR1  CPH1     0.2     4     0.0  ! RNUS
CN7B CN7B NR1  CPH2     0.1     3   180.0  ! RNUS
CN7B CN7B NR1  CPH2     0.3     2     0.0  ! RNUS
CN7B CN7B NR1  CPH2     0.0     1   180.0  ! RNUS

HN7  CN7B NR1  CPH1     0.0     3     0.0  !
HN7  CN7B NR1  CPH2     0.195   3     0.0  !
CN8  CN8  CN7B NR1      0.0     3     0.0
CN7  CN7B CN7B NR1      0.0     3     0.0  ! RNUS
CN8  ON6  CN7B NR1      0.0     3     0.0
HN8  CN8  CN7B NR1      0.0     3     0.0
HN7  CN7B CN7B NR1      0.0     3     0.0  ! RNUS
NR1  CN7B CN7B ON5      0.0     3     0.0  ! RNUS
!-- For imidazole, transferred from imidazole alone:
!CPH2 NR1  CPH1 CPH1    14.0000  2   180.00 ! From imidazole (NF)
!CPH2 NR2  CPH1 CPH1    14.0000  2   180.00 ! From imidazole (NF)
!NR1  CPH1 CPH1 HR3      3.0000  2   180.00 ! From imidazole (NF)
!NR1  CPH2 NR2  CPH1    14.0000  2   180.00 ! From imidazole (NF)
!NR2  CPH1 CPH1 NR1     14.0000  2   180.00 ! From imidazole (NF)
!NR2  CPH2 NR1  CPH1    14.0000  2   180.00 ! From imidazole (NF)
!HR1  CPH2 NR1  CPH1     3.0000  2   180.00 ! From imidazole (NF)
!HR1  CPH2 NR2  CPH1     3.0000  2   180.00 ! From imidazole (NF)
!HR3  CPH1 CPH1 HR3      2.0000  2   180.00 ! From imidazole (NF)
!HR3  CPH1 NR1  CPH2     3.0000  2   180.00 ! From imidazole (NF)
!HR3  CPH1 NR2  CPH2     3.0000  2   180.00 ! From imidazole (NF)
!NR2  CPH1 CPH1 HR3      3.0000  2   180.00 ! From imidazole (NF)

!------------------- added for thf-oh-ch3-im ---------------------
CN7B ON6  CN7  CN9      0.0     3     0.0
CN7  ON6  CN7B NR1      0.0     3     0.0
CN7  ON6B CN7B NR1      0.0     3     0.0 ! RNUS
NR1  CN7B CN8  CN7      0.0     3     0.0
!%%%%%%% new terms for dna and the deoxyribose-based model compounds %%%%%%
! The following is for: THF3P (model for espilon), THFM3P (model for puckering),
! THF5P (model for gamma and beta), THFCH3IM (model for chi), nucleotide analogue
!@@@@@@ Begining of chi
!============= added for torsion about chi in adenine ============
!For link from sugar to base:
CN7B NN2  CN4  HN3       0.3     2       180.0 ! NF
CN7B NN2  CN5  CN5      11.0     2       180.0 ! adm jr.
CN7B NN2  CN4  NN4      11.0     2       180.0 ! adm jr.
CN7B NN2  CN4  NN3A     11.0     2       180.0 ! adm jr.
!For chi itself:
	!DNA:
ON6  CN7B NN2  CN5       1.1     1       180.0 !
ON6  CN7B NN2  CN4       1.1     1         0.0 ! NF 
        !RNA:
ON6B CN7B NN2  CN5       1.1     1       180.0 !
ON6B CN7B NN2  CN4       1.1     1         0.0 !
	!DNA:
CN8  CN7B NN2  CN5       0.3     3         0.0 ! NF
CN8  CN7B NN2  CN4       0.0     3       180.0 ! NF
	!RNA:
CN7B CN7B NN2  CN5       0.3     3         0.0 ! NF
CN7B CN7B NN2  CN4       0.0     3       180.0 ! NF
	!Arabinose:
CN7C CN7B NN2  CN5       0.3     3         0.0 ! 
CN7C CN7B NN2  CN4       0.0     3       180.0 !

HN7  CN7B NN2  CN5       0.0     3         0.0 ! NF
HN7  CN7B NN2  CN4       0.195   3         0.0 ! NF
!@@@@@@ End of chi in adenines 

!============== terms for torsion about chi in cytosines ===========
CN7B NN2  CN3  HN3       0.3     2       180.0 ! NF
CN7B NN2  CN1  ON1C     11.0     2       180.0 ! adm jr. from A
CN7B NN2  CN1  NN3      11.0     2       180.0 ! adm jr. 
CN7B NN2  CN3  CN3      11.0     2       180.0 ! adm jr.
	!DNA:
ON6  CN7B NN2  CN1       0.0     3         0.0 ! 
ON6  CN7B NN2  CN3       1.0     1         0.0 ! NF 
        !RNA:
ON6B CN7B NN2  CN1       0.0     3         0.0 !
ON6B CN7B NN2  CN3       1.0     1         0.0 !
        !DNA:
CN8  CN7B NN2  CN1       1.0     3         0.0 ! 
CN8  CN7B NN2  CN3       0.0     3       180.0 ! NF 030697
        !RNA:
CN7B CN7B NN2  CN1       1.0     3         0.0 !
CN7B CN7B NN2  CN3       0.0     3       180.0 !
	!Arabinose:
CN7C CN7B NN2  CN1       1.0     3         0.0 !
CN7C CN7B NN2  CN3       0.0     3       180.0 !

HN7  CN7B NN2  CN1       0.0     3         0.0 ! NF
HN7  CN7B NN2  CN3       0.195   3         0.0 ! NF
!@@@@@@ End of chi in cytosines 

!=========== terms for torsion about chi in uracils/thymines ===========
CN7B NN2B CN3  HN3       0.3     2       180.0 ! NF
CN7B NN2B CN1T ON1      11.0     2       180.0 ! adm jr. from A
CN7B NN2B CN1T NN2U     11.0     2       180.0 ! adm jr.
CN7B NN2B CN3  CN3T     11.0     2       180.0 ! adm jr.
	!DNA:
ON6  CN7B NN2B CN1       0.0     3         0.0 ! 
ON6  CN7B NN2B CN1T      0.7     3         0.0 ! 
ON6  CN7B NN2B CN1T      0.8     1       180.0 ! 
ON6  CN7B NN2B CN3       0.9     1         0.0 ! NF 
        !RNA:
ON6B CN7B NN2B CN1       0.0     3         0.0 !
ON6B CN7B NN2B CN1T      0.7     3         0.0 !
ON6B CN7B NN2B CN1T      0.8     1       180.0 !
ON6B CN7B NN2B CN3       0.9     1         0.0 !
        !DNA:
CN8  CN7B NN2B CN1T      0.2     3       180.0 ! 
CN8  CN7B NN2B CN3       0.0     3       180.0 ! NF
        !RNA:
CN7B CN7B NN2B CN1T      0.2     3       180.0 !
CN7B CN7B NN2B CN3       0.0     3       180.0 !
	!Arabinose:
CN7C CN7B NN2B CN1T      0.2     3       180.0 !
CN7C CN7B NN2B CN3       0.0     3       180.0 !

HN7  CN7B NN2B CN1T      0.0     3         0.0 ! NF
HN7  CN7B NN2B CN3       0.195   3         0.0 ! NF
!@@@@@@ End of chi in thymines 

!============= added for torsion about chi in guanine ============
CN7B NN2B CN4  HN3       0.3     2       180.0 ! NF
CN7B NN2B CN4  NN4      11.0     2       180.0 ! adm jr.
CN7B NN2B CN5  CN5G     11.0     2       180.0 ! adm jr. from U
CN7B NN2B CN5  NN3G     11.0     2       180.0 ! adm jr.
	!DNA:
ON6  CN7B NN2B CN5       0.2     3         0.0 !
ON6  CN7B NN2B CN5       1.1     1       180.0 !
ON6  CN7B NN2B CN4       1.4     1         0.0 ! NF 
        !RNA:
ON6B CN7B NN2B CN5       0.2     3         0.0 !
ON6B CN7B NN2B CN5       1.1     1       180.0 !
ON6B CN7B NN2B CN4       1.4     1         0.0 !
        !DNA:
CN8  CN7B NN2B CN5       0.0     3         0.0 ! NF
CN8  CN7B NN2B CN4       0.0     3       180.0 ! NF 030697
        !RNA:
CN7B CN7B NN2B CN5       0.0     3         0.0 ! NF
CN7B CN7B NN2B CN4       0.0     3       180.0 !
	!Arabinose:
CN7C CN7B NN2B CN5       0.0     3         0.0 !
CN7C CN7B NN2B CN4       0.0     3       180.0 !

HN7  CN7B NN2B CN5       0.0     3         0.0 ! NF
HN7  CN7B NN2B CN4       0.195   3         0.0 ! NF
!@@@@@@ End of chi in guanines 
!@@@@@@ link (not chi) between base and sugar for both purines and pyrimidines:
	!DNA:
CN7  ON6  CN7B NN2       0.0     3         0.0
CN7  ON6  CN7B NN2B      0.0     3         0.0
	!RNA:
CN7  ON6B CN7B NN2       0.0     3         0.0
CN7  ON6B CN7B NN2B      0.0     3         0.0
        !DNA:
CN7  CN8  CN7B NN2       0.0     3         0.0
CN7  CN8  CN7B NN2B      0.0     3         0.0
HN8  CN8  CN7B NN2       0.0     3         0.0
HN8  CN8  CN7B NN2B      0.0     3         0.0
        !RNA:
CN7  CN7B CN7B NN2       0.0     3         0.0
CN7  CN7B CN7B NN2B      0.0     3         0.0
	!Arabinose:
CN7  CN7C CN7B NN2       0.0     3         0.0
CN7  CN7C CN7B NN2B      0.0     3         0.0
	!RNA
HN7  CN7B CN7B NN2       0.0     3         0.0
HN7  CN7B CN7B NN2B      0.0     3         0.0
	!Arabinose:
HN7  CN7C CN7B NN2       0.0     3         0.0
HN7  CN7C CN7B NN2B      0.0     3         0.0

!@@@@@@ Begining of torsions involving exocyclic sugar atoms:
!======= CN7  CN8B  ON2  P = C4'-C5'-O5'-P 
CN7  CN8B ON2  P        0.2     1       120.0 !bet C4'-C5'-O5'-P, adm jr.
! the following differ significantly from the alcohols
! in the protein (based on ethanol), they also differ from other
! NA C-C-OH-H parameters (see below)
! The two following terms have been replaced by their ethanol 
! counterpart (NF, 083098)
!CN7  CN8B ON5  HN5      0.5     3         0.0 !bet
!CN7  CN8B ON5  HN5      1.0     1         0.0 !bet
! the following would be equivalent to the proteins
CN7  CN8B ON5  HN5      1.3300  1     0.00
CN7  CN8B ON5  HN5      0.1800  2     0.00
CN7  CN8B ON5  HN5      0.3200  3     0.00
!======= HN8  CN8B  ON2 P = H-C5'-O5'-P )beta
HN8  CN8B ON5  HN5      0.0     3         0.0 !bet
!======== CN7 CN7 CN8B ON2 = C3'-C4'-C5'-O5'
! When O5' is ON2 (phosphodiester linkage):
CN7  CN7  CN8B ON2      0.20    4       180.0 !gam adm jr.
CN7  CN7  CN8B ON2      0.80    3       180.0 !gam C3'-C4'-C5'-O5'
CN7  CN7  CN8B ON2      0.40    2         0.0 !gam
CN7  CN7  CN8B ON2      2.50    1       180.0 !gam
! When O5' is ON5 (5TER patch):
CN7  CN7  CN8B ON5      0.20    4       180.0 !gam adm jr.
CN7  CN7  CN8B ON5      0.80    3       180.0 !gam C3'-C4'-C5'-O5'
CN7  CN7  CN8B ON5      0.40    2         0.0 !gam
CN7  CN7  CN8B ON5      2.50    1       180.0 !gam
!======== ON6 CN7 CN8B ON2 = O4'-C4'-C5'-O5'
! When O5' is ON2 (3'-5' phosphodiester linkage)
ON6  CN7  CN8B ON2      3.4     1       180.0 !gam O4'-C4'-C5'-O5',influences +60
ON6B CN7  CN8B ON2      3.4     1       180.0 !gam, RNA
! When O5' is ON5 (5TER patch):
ON6  CN7  CN8B ON5      3.4     1       180.0 !gam
ON6B CN7  CN8B ON5      3.4     1       180.0 !gam, RNA
!======== HN8  CN8B  CN7  CN7 = H-C5'-C4'-H
HN8  CN8B CN7  CN7      0.195   3         0.0 !gam,H-C5'-C4'-H
!======== HN7 CN8B CN7 ON6 = H-C5'-C4'-O4'
HN8  CN8B CN7  ON6      0.195   1         0.0 !gam,H-C5'-C4'-O4'
HN8  CN8B CN7  ON6B     0.195   1         0.0 !gam, RNA
!======== HN7 CN7 CN8B ON2 =  H-C4'-C5'-O5'
! When O5' is ON2 (phosphodiester linkage):
HN7  CN7  CN8B ON2      0.195	3         0.0 !gam H-C4'-C5'-O5'
! When O5' is ON5 (5TER patch):
HN7  CN7  CN8B ON5      0.195   3         0.0 !gam
HN8  CN8  CN8  ON6      0.195   1         0.0 !gam,H-C5'-C4'-O4'

!======== CN8 CN7 CN7 CN8B = C2'-C3'-C4'-C5'
! This term is well suited to modify the puckering surfaces, in 
! particular because it is present in THF5P 
CN8  CN7  CN7  CN8B     0.5     4       180.0 !del lowers 180 deg. 
CN7B CN7  CN7  CN8B     0.2     4       180.0 !del, RNA
CN7C CN7  CN7  CN8B     0.5     4       180.0 !del, arabinose
!======== CN8B CN7 CN7 ON2 = C5'-C4'-C3'-O3' 
! These terms affect the c2endo/c3endo energy difference
! When O3' is ON2 (3'-5' phosphodiester linkage)
ON2  CN7  CN7  CN8B      0.2      4       0.0 !del
! the following term controls the location of the barrier at ~75 deg.
ON2  CN7  CN7  CN8B      0.8      3     180.0 !del,decreases P [100,250]
! When O3' is ON5 (patch 3TER) 
ON5  CN7  CN7  CN8B      0.2      4       0.0 !
ON5  CN7  CN7  CN8B      0.8      3     180.0 !
!======== ON6 CN7 CN7 ON2 = O4'-C4'-C3'-O3' 
! These terms contribute to delta
! These terms are present in THF3P and THFM3P but not in THF5P
! When O3' is ON2 (3'-5' phosphodiester linkage)
ON2  CN7  CN7  ON6       0.5     6        0.0 !del, good for amplitudes
ON2  CN7  CN7  ON6       0.3     5        0.0 !del, impact on amplitudes
ON2  CN7  CN7  ON6       0.6     4      180.0 !del, increases c2'endo
ON2  CN7  CN7  ON6       0.2     3        0.0 !
ON2  CN7  CN7  ON6B      0.4     6        0.0 !del, RNA, good for amplitudes
ON2  CN7  CN7  ON6B      0.0     5        0.0 !del, RNA, impact on amplitudes
ON2  CN7  CN7  ON6B      0.0     4      180.0 !del, RNA, increases c2'endo
ON2  CN7  CN7  ON6B      1.6     3        0.0 !del, RNA, increases C2'endo
! for ndph: make identical to ON2  CN7  CN7  ON6B
ON2  CN7B CN7B ON6B      0.4     6        0.0 !del, RNA, good for amplitudes
ON2  CN7B CN7B ON6B      0.0     5        0.0 !del, RNA, impact on amplitudes
ON2  CN7B CN7B ON6B      0.0     4      180.0 !del, RNA, increases c2'endo
ON2  CN7B CN7B ON6B      1.6     3        0.0 !del, RNA, increases C2'endo
! When O3' is ON5 (patch 3TER)
ON5  CN7  CN7  ON6       0.5     6        0.0 !  
ON5  CN7  CN7  ON6       0.3     5        0.0 !  
ON5  CN7  CN7  ON6       0.6     4      180.0 !  
ON5  CN7  CN7  ON6       0.2     3        0.0 ! 
ON5  CN7  CN7  ON6B      0.4     6        0.0 !RNA
ON5  CN7  CN7  ON6B      0.0     5        0.0 !RNA
ON5  CN7  CN7  ON6B      0.0     4      180.0 !RNA
ON5  CN7  CN7  ON6B      1.6     3        0.0 !RNA. increases c2'endo

!======== CN8B CN7 ON6 CN7B = C5'-C4'-O4'-C1' 
! This term can be used to adjust the c2'endo/c3'endo  
! energy difference in THF5P
CN7B ON6  CN7  CN8B      0.8     3         0.0 ! P [30,80] 
CN7B ON6B CN7  CN8B      2.0     3         0.0 ! To lower barrier in RNA
!======== ON2 CN7 CN8 CN7B = O3'-C3'-C2'-C1' 
! This term can be used to adjust the c2'endo/c3'endo
! When O3' is ON2 
ON2  CN7  CN8  CN7B      0.8     6         0.0 !  
ON2  CN7  CN8  CN7B      0.4     5         0.0 ! Moves the barrier right 
ON2  CN7  CN8  CN7B      2.0     3       180.0 !  
ON2  CN7  CN7B CN7B      0.6     6         0.0 ! RNA
ON2  CN7  CN7B CN7B      0.0     5         0.0 ! RNA c2/c3 endo in RNA 
ON2  CN7  CN7B CN7B      1.6     3       180.0 !
ON2  CN7  CN7C CN7B      0.8     6         0.0 ! Arabinose (from DNA)
ON2  CN7  CN7C CN7B      0.4     5         0.0 ! 
ON2  CN7  CN7C CN7B      2.0     3       180.0 !
!When O3' is ON5 (patch 3TER)
ON5  CN7  CN8  CN7B      0.8     6         0.0 !
ON5  CN7  CN8  CN7B      0.4     5         0.0 !
ON5  CN7  CN8  CN7B      2.0     3       180.0 !
ON5  CN7  CN7B CN7B      0.6     6         0.0 ! RNA, c2/c3 endo
ON5  CN7  CN7B CN7B      0.0     5         0.0 ! RNA
ON5  CN7  CN7B CN7B      1.6     3       180.0 ! RNA
ON5  CN7  CN7C CN7B      0.8     6         0.0 ! Arabinose (from DNA)
ON5  CN7  CN7C CN7B      0.4     5         0.0 ! Arabinose (from DNA)
ON5  CN7  CN7C CN7B      2.0     3       180.0 ! Arabinose (from DNA)
!======== ON2 CN7 CN8 HN8 = O3'-C3'-C2'-H 
ON2  CN7  CN8  HN8       0.195   3         0.0 ! 
ON5  CN7  CN8  HN8       0.195   3       180.0 !
ON2  CN7  CN7B HN7       0.195   3         0.0 ! RNA
ON5  CN7  CN7B HN7       0.195   3       180.0 ! RNA
ON2  CN7  CN7C HN7       0.195   3         0.0 ! Arabinose (from DNA)
ON5  CN7  CN7C HN7       0.195   3       180.0 ! Arabinose (from DNA)
!======== HN7 CN7 CN7 ON2 = H-C4'-C3'-O3' 
HN7  CN7  CN7  ON2       0.195   3         0.0
HN7  CN7  CN7  ON5       0.195   3         0.0
!======== CN7 CN7 ON2 P = C4'-C3'-O3'-P 
CN7  CN7  ON2  P         0.6     5         0.0 !eps
CN7  CN7  ON2  P         0.2     4         0.0 !eps, locat of 200 mimima
CN7  CN7  ON2  P         0.0     3       180.0 !eps, barE beteen minima
CN7  CN7  ON2  P         0.4     2         0.0 !eps, relE of 200 vs 275 min
CN7  CN7  ON2  P         1.9     1       180.0 !eps
!======== CN8 CN7 ON2 P = C2'-C3'-O3'-P 
! This term is involved in epsilon
CN8  CN7  ON2  P         2.5     1       180.0 !eps
CN7B CN7  ON2  P         2.5     1       180.0 !eps, RNA 
CN7B CN7B ON2  P         2.5     1       180.0 !eps, NADPH
CN7  CN7B ON2  P         2.5     1       180.0 !eps, NADPH
CN7C CN7  ON2  P         2.5     1       180.0 !eps, Arabinose (from DNA)
! base on thfalloh
! the following differ significantly from the protein based
! alcohol parameters (based on ethanol, see above)
CN7  CN7  ON5  HN5       0.5     3         0.0
CN7  CN7  ON5  HN5       0.3     2       180.0
CN7  CN7  ON5  HN5        1.5     1        0.0
CN8  CN7  ON5  HN5       0.5     3         0.0
CN8  CN7  ON5  HN5       1.0     2       180.0
CN8  CN7  ON5  HN5       0.3     1         0.0
CN7B CN7  ON5  HN5       0.8     3         0.0 ! RNA
CN7B CN7  ON5  HN5       0.5     1         0.0 ! RNA
CN7C CN7  ON5  HN5       0.8     3         0.0 ! Arabinose (from DNA)
CN7C CN7  ON5  HN5       0.5     1         0.0 ! Arabinose (from DNA)
! Was simply transfered from HN7  CN7  ON2  P
! adm jr. should convert to alcohol term (see ribose etc)
HN7  CN7  ON5  HN5       0.0     3         0.0
HN7  CN7  CN8B HN8       0.195   3         0.0 !gam H-C4'-C5'-H
HN7  CN7  CN7  CN8B      0.195   3         0.0 !gam H-C3'-C4'-C5'
!@@@@@@ End of torsions involving exocyclic atoms:
!@@@@@@ Begining of torsions for endocyclic atoms only:
CN8  CN7B ON6  CN7       0.6     6       180.0 !C2'-C1'-O4'-C4'
CN8  CN7  CN7  ON6       0.0     3         0.0 !C2'-C3'-C4'-O4'
CN7B CN7B ON6B CN7       0.0     6         0.0 ! RNA, Lowers barrier
CN7B CN7  CN7  ON6B      0.0     3         0.0 ! RNA
CN7C CN7B ON6  CN7       0.6     6       180.0 ! Arabinose (from DNA)
CN7C CN7  CN7  ON6       0.0     3         0.0 ! Arabinose (from DNA)
!======== CN7 CN8 CN7B ON6 for nucleosides, transfered from =========
!======== CN7 CN8  CN8  ON6 from thfoh ==============================
CN7  CN8  CN7B ON6       0.6     6         0.0 ! C3'-C2'-C1'-O4', adjust barrier
CN7  CN7B CN7B ON6B      0.4     6         0.0 ! RNA
CN7  CN7C CN7B ON6       0.6     6         0.0 ! Arabinose (from DNA)
!======== C1'-C2'-C3'-C4' ========
CN7B CN8  CN7  CN7       0.4      6        0.0 ! good for amplitudes
CN7B CN7B CN7  CN7       0.0      6        0.0 ! RNA
CN7B CN7C CN7  CN7       0.4      6        0.0 ! Arabinose (from DNA)
!======== CN7 CN7 ON6 CN7B for nucleosides, transfered from ========
!======== CN7 CN7 ON6 CN8 from thfohch3 ============================
CN7  CN7  ON6  CN7B      0.6      6      180.0 ! C3'-C4'-O4'-C1'
CN7  CN7  ON6B CN7B      0.0      6      180.0 ! RNA
!======== Directly adjusted with TM3P
HN7  CN7  CN7  CN8       0.0      3        0.0 !puc,H-C3'-C4'-C5'
HN7  CN7  CN7  CN7C      0.0      3        0.0 ! Arabinose (from DNA)
!======== HN7 CN7 CN7 ON6 = H-C2'-C3'-O4'
HN7  CN7  CN8  CN7B      0.195    3       0.0 !H-C3'-C2'-C1'
HN7  CN7B CN8  CN7       0.195    3       0.0 !H-C1'-C2'-C3'
HN7  CN7  CN7  ON6       0.195    3     180.0 ! useful
HN8  CN8  CN7B ON6       0.195    3       0.0 !H-C2'-C1'-O4'
HN7  CN7  CN7  HN7       0.195    3       0.0 !H-C4'-C3'-H
HN7  CN7B CN8  HN8       0.195    3       0.0 !H-C1'-C2'-H 
HN7  CN7  CN8  HN8       0.195    3       0.0 !H-C3'-C2'-H
HN8  CN8  CN7  CN7       0.195    3       0.0 ! useful *cccc*
HN7  CN7  ON6  CN7B      0.195    3       0.0 !H-C3'-C2'-C1'
HN7  CN7B ON6  CN7       0.000    3       0.0 !H-C1'-O4'-C4'
HN7  CN7  CN7  ON6B      0.195    3     180.0 ! RNA
HN8  CN8  CN7B ON6B      0.195    3       0.0 ! RNA
HN7  CN7B ON6B CN7       0.000    3       0.0 ! RNA
HN7  CN7  ON6B CN7B      0.195    3       0.0 ! RNA
HN7  CN7  CN7B CN7B      0.195    3       0.0 ! RNA, H-C3'-C2'-C1'
HN7  CN7B CN7B CN7       0.195    3       0.0 ! RNA, H-C1'-C2'-C3'
HN7  CN7B CN7B ON6B      0.195    3       0.0 ! RNA, H-C2'-C1'-O4'
HN7  CN7  CN7C CN7B      0.195    3       0.0 !Arabinose (from DNA), H-C3'-C2'-C1'
HN7  CN7B CN7C CN7       0.195    3       0.0 !Arabinose (from DNA), H-C1'-C2'-C3'
HN7  CN7C CN7B ON6       0.195    3       0.0 !Arabinose (from DNA), H-C2'-C1'-O4'
HN7  CN7B CN7C HN7       0.195    3       0.0 !Arabinose (from DNA), H-C1'-C2'-H
HN7  CN7  CN7C HN7       0.195    3       0.0 !Arabinose (from DNA), H-C3'-C2'-H
HN7  CN7C CN7  CN7       0.195    3       0.0 !Arabinose (from DNA), useful *cccc*
!@@@@@@ End of torsions for endocyclic atoms only

!@@@@@@ Begining of orsions specifically defined for RNA @@@@@@
! N9-C1'-C2'-O2':
NN2  CN7B CN7B ON5      0.000    3       0.0 ! Adenine and cytosine
NN2B CN7B CN7B ON5      0.000    3       0.0 ! Guanine and uracil
ON5  CN7B CN7B HN7       0.000   3       0.0 ! 
HN7  CN7B CN7B HN7       0.000   3       0.0 ! 
CN7  CN7  CN7B ON5        0.000   3       0.0
ON6B CN7B CN7B ON5        0.000   3       0.0
ON5  CN7B CN7  ON2        0.000   3       0.0
! for ndph
ON5  CN7  CN7B ON2        0.000   3       0.0
ON5  CN7B CN7  ON5        0.000   3       0.0
HN7  CN7B ON5  HN5        0.000   3       0.0
! the following differ significantly from the protein based
! alcohol parameters (based on ethanol, see above)
HN5  ON5  CN7B CN7B       0.000   6     180.0 !
HN5  ON5  CN7B CN7B       0.800   3       0.0 !
HN5  ON5  CN7B CN7B       0.000   2     180.0 !
HN5  ON5  CN7B CN7B       0.000   1     180.0 !
HN5  ON5  CN7B CN7        0.300   3       0.0 ! 030298
HN5  ON5  CN7B CN7        0.000   1       0.0 ! 030298
!@@@@@@ End of torsions specifically defined for RNA @@@@@@

!@@@@@@ Begining of torsions specifically defined for arabinose @@@@@@
ON6  CN7B CN7C ON5       0.000   3       0.0
! the following differ significantly from the protein based
! alcohol parameters (based on ethanol, see above)
CN7B CN7C ON5  HN5       0.000   3       0.0
CN7  CN7C ON5  HN5       0.000   3       0.0
HN7  CN7B CN7C ON5       0.000   3       0.0
CN7  CN7  CN7C ON5       0.000   3       0.0
HN7  CN7C ON5  HN5       0.000   3       0.0
ON5  CN7C CN7  HN7       0.000   3       0.0
ON5  CN7C CN7  ON2       0.000   3       0.0
!@@@@@@ End of torsions specifically defined for arabinose @@@@@@

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
!
!from lipids
OBL  X    X    CL         100.00    0     0.00 ! acetic acid
HEL2 HEL2 CEL2 CEL2         3.00    0     0.00 ! ethene, yin,adm jr., 12/95
OCL  X    X    CL          96.00    0     0.00 ! acetate

! from CHARMM23 guesses parameters
! Rommie Jerome

CC   O    NH2  CPH1 900.000   0.000    0
CPH1 CPH1 NR2  CC 900.000   0.000    0
NH2  H    H    CC 0.000   0.000    0
CPH1 CPH1 NR1  NC2 900.000   0.000    0
NR1  CPH1 CPH2 CN7B  0.000   100.000    0
C    NC2  NC2  HC  5.000   0.000    0

! Added for CYG residue
! by Rommie 04-14-03

CD  OB  OH1  CT1   0.00   0.00  0.00 


! END OF CHARMM-GUESSED PARAMETERS
!
CPB  CPA  NPH  CPA    20.8000         0      0.0000 ! ALLOW HEM
                ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB  X    X    C      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)
!nucleic acid section
!
HN2  X    X    NN2      1.0     0     0.0     !C, adm jr. 11/97
NN2B CN4  CN5  HN2      7.0     0     0.0     !G, adm jr. 11/97
NN2G CN4  CN1  HN2      0.8     0     0.0     !Inosine, adm jr. 2/94
HN1  X    X    NN1      4.0     0     0.0     !G, adm jr. 11/97
NN1  CN2  HN1  HN1      6.0     0     0.0     !A,C adm jr. 11/97
CN1  X    X    ON1     90.0     0     0.0     !U
CN1T X    X    ON1     90.0     0     0.0     !U
CN1  NN2G CN5G ON1     90.0     0     0.0     !G
CN1T NN2B NN2U ON1    110.0     0     0.0     !T/O2, adm jr. 11/97
CN1  NN2U CN3T ON1     90.0     0     0.0     !T/O4, adm jr. 11/97
CN1  X    X    ON1C    80.0     0     0.0     !C, par_32, adm jr. 10/2/91
CN2  X    X    NN1     90.0     0     0.0     !C, 
CN2  NN3G NN2G NN1     40.0     0     0.0     !G
CN2  NN3A CN5  NN1     40.0     0     0.0     !A
CN2  NN3  CN3  NN1     60.0     0     0.0     !C, 
CN4  NN2G NN3I HN3     39.0     0     0.0     !Inosine, adm jr. 2/94
CN9  X    X    CN3T    14.0     0     0.0     !T, adm jr. 11/97
! nicotinamide adenine dinucleotide                                             
CN3  CN3C CN8  HN6     15.0     0     0.0  !nich, jjp1/adm jr.
HN3B X    X    CN3     15.0     0     0.0  !nad/ppi, jjp1/adm jr.
HN3B X    X    CN3A    13.0     0     0.0  !nad/ppi, jjp1/adm jr.
HN3B X    X    CN3B    13.0     0     0.0  !nad/ppi, jjp1/adm jr.
HN2  CN3  CN3B NN2     50.0     0     0.0  !nad/ppi, jjp1/adm jr.
HN1  HN1  CN1A NN1     -5.0     0     0.0  !nad/ppi, jjp1/adm jr.
ON1  X    X    CN1A    40.0     0     0.0  !nad/ppi, jjp1/adm jr.
HN3  X    X    CN3C    53.0     0     0.0  !nad/ppi, jjp1/adm jr.
HN6  X    X    CN3C    53.0     0     0.0  !nich, adm jr.
HN8  CN3  CN3  CN8     18.0     0     0.0  !nad/ppi, jjp1/adm jr.
!================== new terms added for sugar model compounds =========
!----------------------- Added for imidazole --------------------
!HR1  NR1  NR2  CPH2    0.50         0      0.00 ! From imidazole (NF)
!HR1  NR2  NR1  CPH2    0.50         0      0.00 ! From imidazole (NF)
!HR3  CPH1 NR1  CPH1    0.50         0      0.00 ! From imidazole (NF)
!HR3  CPH1 NR2  CPH1    0.50         0      0.00 ! From imidazole (NF)
!HR3  NR1  CPH1 CPH1    0.50         0      0.00 ! From imidazole (NF)
!HR3  NR2  CPH1 CPH1    0.50         0      0.00 ! From imidazole (NF)
!NR1  CPH1 CPH2 CN7B    0.60         0      0.00 ! From imidazole (NF), k increased
!NR1  CPH2 CPH1 CN7B    0.60         0      0.00 ! From imidazole (NF), k increased

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
!
! from lipids

HOL      0.0       -0.046     0.2245
HAL1     0.0       -0.022     1.3200 ! alkane, 3/92
HAL2     0.0       -0.028     1.3400 ! alkane, yin and mackerell, 4/98
HAL3     0.0       -0.024     1.3400 ! alkane, yin and mackerell, 4/98
HCL      0.0       -0.046     0.2245 ! ethanolamine
!HT       0.0       -0.046     0.2245
HL       0.0       -0.046     0.7    ! polar H on NC4+
HEL1     0.0       -0.031     1.25   ! alkene, yin,adm jr., 12/95
HEL2     0.0       -0.026     1.26   ! alkene, yin,adm jr., 12/95
!
CL       0.0       -0.070     2.00   ! methyl acetate update
CTL1     0.0       -0.0200    2.275 0.0 -0.01 1.9 ! alkane, 3/92
CTL2     0.0       -0.0560    2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
CTL3     0.0       -0.0780    2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
CTL5     0.0       -0.0800    2.06  0.0 -0.01 1.9 ! old CTL3
                                                  ! maintained for tetramethylammonium
CEL1     0.0       -0.068     2.09   ! alkene, yin,adm jr., 12/95
CEL2     0.0       -0.064     2.08   ! alkene, yin,adm jr., 12/95
!
OBL      0.0       -0.12      1.70  0.0 -0.12 1.4
OCL      0.0       -0.12      1.70
O2L      0.0       -0.12      1.70
OHL      0.0       -0.1521    1.77
OSL      0.0       -0.1521    1.77
!OT       0.0       -0.1521    1.7682
!
NH3L     0.0       -0.20      1.85  ! ethanolamine
NTL      0.0       -0.20      1.85  ! as all other nitogens
!
SL       0.0       -0.47      2.1   ! methylsulfate
PL       0.0       -0.585     2.15  ! ADM Jr.

!
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
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
! carbon wildcards, following atom order is essential for accurate results
!C*     0.000000  -0.070000     2.000000
!CP%    0.000000  -0.090000     1.800000
!C%1    0.000000  -0.020000     2.275000   0.000000  -0.010000     1.900000
!C%2    0.000000  -0.055000     2.175000   0.000000  -0.010000     1.900000
!C%3    0.000000  -0.080000     2.060000   0.000000  -0.010000     1.900000
!CPH+   0.000000  -0.050000     1.800000
!C      0.000000  -0.110000     2.000000
!CA     0.000000  -0.070000     1.992400
!CE1    0.000000  -0.068000     2.090000
!CE2    0.000000  -0.064000     2.080000
!CM     0.000000  -0.110000     2.100000
!CP3    0.000000  -0.055000     2.175000   0.000000  -0.010000     1.900000 ! ALLOW   ALI
!CPT    0.000000  -0.090000     1.800000   0.000000  -0.090000     1.900000
!CS     0.000000  -0.110000     2.200000
!CY     0.000000  -0.070000     1.992400

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
! hydrogen wildcards
!H*     0.000000  -0.046000     0.224500 
!HA     0.000000  -0.022000     1.320000 
!HE1    0.000000  -0.031000     1.250000 
!HE2    0.000000  -0.026000     1.260000 
!HB     0.000000  -0.022000     1.320000 
!HP     0.000000  -0.030000     1.358200   0.000000  -0.030000     1.358200
!HR1    0.000000  -0.046000     0.900000 
!HR2    0.000000  -0.046000     0.700000 
!HR3    0.000000  -0.007800     1.468000 
!HS     0.000000  -0.100000     0.450000 
!
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
! nitrogen wildcards
!N*     0.000000  -0.200000     1.850000 
!N      0.000000  -0.200000     1.850000   0.000000  -0.000100     1.850000 
!NH1    0.000000  -0.200000     1.850000   0.000000  -0.200000     1.550000 
!
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
OT     0.000000  -0.152100     1.768200 ! ALLOW   WAT
                !TIP3P OXYGEN PARAMETERS, adm jr., NBFIX obsolete
! oxygen wildcards
!O*     0.000000  -0.120000     1.700000   0.000000  -0.120000     1.400000
!OC     0.000000  -0.120000     1.700000
!OH1    0.000000  -0.152100     1.770000
!OM     0.000000  -0.120000     1.700000
!OS     0.000000  -0.152100     1.770000
!OT     0.000000  -0.152100     1.768200

!CAL    0.000000  -0.120000     1.710000 ! ALLOW ION
!                !Calcium (BP)
FE     0.010000   0.000000     0.650000 ! ALLOW HEM
                ! Heme (6-liganded): Iron atom (KK 05/13/91)
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
ZN     0.000000  -0.250000     1.090000 ! ALLOW  ION
                ! RHS March 18, 1990
DUM    0.000000  -0.000000     0.000000 !
                ! dummy atom
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
!nucleic acid section
!HT       0.0       -0.0460    0.2245 ! TIP3P
HN1      0.0       -0.0460    0.2245 
HN2      0.0       -0.0460    0.2245 
HN3      0.0       -0.046     1.1000 !adm jr. aromatic Hvdw 
HNP      0.0       -0.03      1.3582 !JES 8/25/89 values from Jorgensen fit to hydration energy
HN3B     0.0       -0.046     0.9000 !nad/ppi, jjp1/adm jr.
HN3C     0.0       -0.03      1.3582 !check
HN4      0.0       -0.0460    0.2245
HN5      0.0       -0.0460    0.2245
HN6      0.0       -0.0220    1.3200
HN7      0.0       -0.0220    1.3200
HN8      0.0       -0.0280    1.3400 ! Hydrogen bound to CN8
HN9      0.0       -0.0240    1.3400 ! Hydrogen bound to CN9
HNE1     0.0       -0.031     1.25   ! alkene, yin,adm jr., 12/95
HNE2     0.0       -0.026     1.26   ! alkene, yin,adm jr., 12/95
!
! hydrogen wildcards
!HN*      0.0       -0.0460    0.2245 ! HN1, HN2, HN4, HN5
!HN3      0.0       -0.0220    1.1000
!HN3B     0.0       -0.046     0.9000 ! nad/ppi, jjp1/adm jr.
!HN6      0.0       -0.0220    1.3200
!HN7      0.0       -0.0220    1.3200
!HT       0.0       -0.0460    0.2245 ! TIP3P
!                           
NN1      0.0        -0.20     1.85
NN1C     0.0        -0.20     1.85
NN2      0.0        -0.20     1.85
NN2B     0.0        -0.20     1.85 ! From NN2, for N9 in guanines
NN2C     0.0        -0.20     1.85 !
NN2G     0.0        -0.20     1.85
NN2U     0.0        -0.20     1.85
NN3      0.0        -0.20     1.85
NN3A     0.0        -0.20     1.85 
NN3G     0.0        -0.20     1.85 
NN3I     0.0        -0.20     1.85 
NN4      0.0        -0.20     1.85
NN5      0.0        -0.20     1.85
NN6      0.0        -0.20     1.85
!
! nitrogen wildcards
!NN*      0.0        -0.20     1.85  ! all nitrogens
!
ON1      0.0       -0.1200    1.70  
ON1C     0.0       -0.1200    1.70 
ON2      0.0       -0.1521    1.77   
ON2b     0.0       -0.1521    1.77
ON3      0.0       -0.1200    1.70  
ON4      0.0       -0.1521    1.77  
ON5      0.0       -0.1521    1.77  
ON6      0.0       -0.1521    1.77  
ON6B     0.0       -0.1521    1.77  
!OT       0.0       -0.1521    1.7682 ! TIP3P
!
! oxygen wildcards
!ON*      0.0       -0.1521    1.77  ! types ON2, ON4, ON5, ON6 and ON6B
!ON1*     0.0       -0.1200    1.70  ! types ON1 and ON1C
!ON3      0.0       -0.1200    1.70
!OT       0.0       -0.1521    1.7682 ! TIP3P
!
! base ring C vdw param, 11/14/97, adm jr
CN1      0.0       -0.10      1.9000
CN1A     0.0       -0.07      2.0000 ! nad/ppi, jjp1/adm jr. (protein CC)
CN1T     0.0       -0.10      1.9000
CN2      0.0       -0.10      1.9000
CN3      0.0       -0.09      1.9000
CN3A     0.0       -0.18      1.8000 ! nad/ppi, jjp1/adm jr.
CN3B     0.0       -0.18      1.8000 ! nad/ppi, jjp1/adm jr.
CN3C     0.0       -0.18      1.8000 ! nad/ppi, jjp1/adm jr.
CN3D     0.0       -0.09      1.9000 ! 5mc, adm jr.
CN3T     0.0       -0.09      1.9000 ! T, adm jr.
CN4      0.0       -0.075     1.9000
CN5      0.0       -0.075     1.9000
CN5G     0.0       -0.075     1.9000
CN7      0.0       -0.02      2.275  0.0   -0.01 1.90 !equivalent to protein CT1
CN7B     0.0       -0.02      2.275  0.0   -0.01 1.90 !equivalent to protein CT1
CN7C     0.0       -0.02      2.275  0.0   -0.01 1.90 !equivalent to protein CT1
CN7D     0.0       -0.02      2.275  0.0   -0.01 1.90 !equivalent to protein CT1
! alkane optimized terms below, Yin and MacKerell, 1998, JCC, In press
CN8      0.0       -0.0560    2.010  0.0   -0.01 1.90 !
CN8B     0.0       -0.0560    2.010  0.0   -0.01 1.90 !
CN9      0.0       -0.0780    2.040  0.0   -0.01 1.90 !
!
CNE1     0.0       -0.068     2.09   ! alkene, yin,adm jr., 12/95
CNE2     0.0       -0.064     2.08   ! alkene, yin,adm jr., 12/95
CNA      0.0       -0.07      1.9924 !benzene (JES)
CNA2     0.0       -0.07      1.90   !dft, adm jr.
!
! carbon wildcards
!CN*      0.0       -0.10      1.8000 ! CN1, CN2,
!CN1A     0.0       -0.07      2.0000 ! nad/ppi, jjp1/adm jr. (protein CC)
!CN3*     0.0       -0.09      1.8000 ! CN3, CN3A, CN3B, CN3C, CN3D
!CN4      0.0       -0.075     1.8000
!CN5      0.0       -0.075     1.8000
!CN7*     0.0       -0.02      2.2750 0.0 -0.01 1.90 !equivalent to protein CT1
!CN8*     0.0       -0.0560    2.010  0.0 -0.01 1.90 !
!CN9      0.0       -0.0780    2.040  0.0 -0.01 1.90 !
!
FN1      0.0       -0.09      1.70  !aliphatic F for sugars, preliminary from 
                                    !Yin Thesis
FNA      0.0       -0.12      1.70  !aromatic F, 1,3-difluorobenzene pure solvent
!
P        0.0       -0.585     2.15  
P2       0.0       -0.585     2.15  ! nad/ppi, jjp1/adm jr.
! phosphate wildcards
!P*       0.0       -0.585     2.15  ! P and P2
!
!-------------- for imidazole --------------
!CPH1   0.000000  -0.050000     1.800000 ! From imidazole (NF)
!CPH2   0.000000  -0.050000     1.800000 ! From imidazole (NF)
!NR1    0.000000  -0.200000     1.850000 ! From imidazole (NF)
!NR2    0.000000  -0.200000     1.850000 ! From imidazole (NF)
!HR3    0.000000  -0.007800     1.468000 ! From imidazole (NF)
!HR1    0.000000  -0.046000     0.900000 ! From imidazole (NF)
!
! ions
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
MG       0.0       -0.0150    1.18500   ! Magnesium
                   ! B. Roux dA = -441.65
CES      0.0       -0.1900    2.100
                   ! Cesium, so far untested.
!DUM      0.0       -0.000     1.00  ! dummy atom
!

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
