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Commit d1afc976 authored by peastman's avatar peastman
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Merge pull request #1173 from mj-harvey/charmm-permissive 

Add permissive flag to permit undefined atomtypes when reading charmm parameter files
parents f8ef61c0 50088908
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Showing with 66213 additions and 6 deletions
wrappers/python/CMakeLists.txt
View file @ d1afc976
...@@ -69,6 +69,7 @@ foreach(SUBDIR ${SUBDIRS}) ...@@ -69,6 +69,7 @@ foreach(SUBDIR ${SUBDIRS})
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.str" "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.str"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*psf" "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*psf"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/charmm22.*" "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/charmm22.*"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/par*.inp"
) )
foreach(file ${STAGING_INPUT_FILES1}) foreach(file ${STAGING_INPUT_FILES1})
set(STAGING_INPUT_FILES ${STAGING_INPUT_FILES} "${file}") set(STAGING_INPUT_FILES ${STAGING_INPUT_FILES} "${file}")
......
wrappers/python/simtk/openmm/app/charmmparameterset.py
View file @ d1afc976
...@@ -100,7 +100,7 @@ class CharmmParameterSet(object): ...@@ -100,7 +100,7 @@ class CharmmParameterSet(object):
except ValueError: except ValueError:
raise CharmmFileError('Could not convert %s to %s' % (msg, type)) raise CharmmFileError('Could not convert %s to %s' % (msg, type))
def __init__(self, *args): def __init__(self, *args, **kwargs):
# Instantiate the list types # Instantiate the list types
self.atom_types_str = dict() self.atom_types_str = dict()
self.atom_types_int = dict() self.atom_types_int = dict()
...@@ -135,12 +135,17 @@ class CharmmParameterSet(object): ...@@ -135,12 +135,17 @@ class CharmmParameterSet(object):
raise TypeError('Unrecognized file type: %s' % arg) raise TypeError('Unrecognized file type: %s' % arg)
else: else:
raise TypeError('Unrecognized file type: %s' % arg) raise TypeError('Unrecognized file type: %s' % arg)
permissive=kwargs.pop("permissive", False)
if len(kwargs):
raise TypeError('Unrecognised named argument')
for top in tops: self.readTopologyFile(top) for top in tops: self.readTopologyFile(top)
for par in pars: self.readParameterFile(par) for par in pars: self.readParameterFile(par, permissive=permissive)
for strf in strs: self.readStreamFile(strf) for strf in strs: self.readStreamFile(strf)
@classmethod @classmethod
def loadSet(cls, tfile=None, pfile=None, sfiles=[]): def loadSet(cls, tfile=None, pfile=None, sfiles=[], permissive=False):
""" """
Instantiates a CharmmParameterSet from a Topology file and a Parameter Instantiates a CharmmParameterSet from a Topology file and a Parameter
file (or just a Parameter file if it has all information) file (or just a Parameter file if it has all information)
...@@ -149,6 +154,8 @@ class CharmmParameterSet(object): ...@@ -149,6 +154,8 @@ class CharmmParameterSet(object):
- tfile (str) : Name of the Topology (RTF/TOP) file - tfile (str) : Name of the Topology (RTF/TOP) file
- pfile (str) : Name of the Parameter (PAR) file - pfile (str) : Name of the Parameter (PAR) file
- sfiles (list of str) : List or tuple of stream (STR) file names. - sfiles (list of str) : List or tuple of stream (STR) file names.
- permissive (bool) : Accept non-bonbded parameters for undefined
atom types (default False)
Returns: Returns:
New CharmmParameterSet populated with the parameters found in the New CharmmParameterSet populated with the parameters found in the
...@@ -165,7 +172,7 @@ class CharmmParameterSet(object): ...@@ -165,7 +172,7 @@ class CharmmParameterSet(object):
if tfile is not None: if tfile is not None:
inst.readTopologyFile(tfile) inst.readTopologyFile(tfile)
if pfile is not None: if pfile is not None:
inst.readParameterFile(pfile) inst.readParameterFile(pfile, permissive=permissive)
if isinstance(sfiles, str): if isinstance(sfiles, str):
# The API docstring requests a list, but allow for users to pass a # The API docstring requests a list, but allow for users to pass a
# string with a single filename instead # string with a single filename instead
...@@ -175,7 +182,7 @@ class CharmmParameterSet(object): ...@@ -175,7 +182,7 @@ class CharmmParameterSet(object):
inst.readStreamFile(sfile) inst.readStreamFile(sfile)
return inst return inst
def readParameterFile(self, pfile): def readParameterFile(self, pfile, permissive=False):
""" """
Reads all of the parameters from a parameter file. Versions 36 and Reads all of the parameters from a parameter file. Versions 36 and
later of the CHARMM force field files have an ATOMS section defining later of the CHARMM force field files have an ATOMS section defining
...@@ -184,6 +191,8 @@ class CharmmParameterSet(object): ...@@ -184,6 +191,8 @@ class CharmmParameterSet(object):
Parameters: Parameters:
- pfile (str) : Name of the CHARMM PARameter file to read - pfile (str) : Name of the CHARMM PARameter file to read
- permissive (bool) : Accept non-bonbded parameters for undefined
atom types (default False)
Notes: The atom types must all be loaded by the end of this routine. Notes: The atom types must all be loaded by the end of this routine.
Either supply a PAR file with atom definitions in them or read in a Either supply a PAR file with atom definitions in them or read in a
...@@ -477,6 +486,23 @@ class CharmmParameterSet(object): ...@@ -477,6 +486,23 @@ class CharmmParameterSet(object):
if current_cmap is not None: if current_cmap is not None:
ty = CmapType(current_cmap_res, current_cmap_data) ty = CmapType(current_cmap_res, current_cmap_data)
self.cmap_types[current_cmap] = ty self.cmap_types[current_cmap] = ty
# If in permissive mode create an atomtype for every type used in
# the nonbonded parameters. This is a work-around for when all that's
# available is a CHARMM22 inp file, which has no ATOM/MASS fields
if permissive:
try:
idx = max(self.atom_types_int.keys())+1000
except ValueError:
idx = 10000
for key in nonbonded_types:
if not key in self.atom_types_str:
atype =AtomType(name=key, number=idx, mass= float('NaN'), atomic_number= 1 )
self.atom_types_str[key] = atype
self.atom_types_int[idx] = atype
idx=idx+1
# Now we're done. Load the nonbonded types into the relevant AtomType # Now we're done. Load the nonbonded types into the relevant AtomType
# instances. In order for this to work, all keys in nonbonded_types # instances. In order for this to work, all keys in nonbonded_types
# must be in the self.atom_types_str dict. Raise a RuntimeError if this # must be in the self.atom_types_str dict. Raise a RuntimeError if this
...@@ -487,6 +513,7 @@ class CharmmParameterSet(object): ...@@ -487,6 +513,7 @@ class CharmmParameterSet(object):
except KeyError: except KeyError:
raise RuntimeError('Atom type %s not present in AtomType list' % raise RuntimeError('Atom type %s not present in AtomType list' %
key) key)
if parameterset is not None: self.parametersets.append(parameterset) if parameterset is not None: self.parametersets.append(parameterset)
if own_handle: f.close() if own_handle: f.close()
......
wrappers/python/tests/TestCharmmFiles.py
View file @ d1afc976
...@@ -142,6 +142,43 @@ class TestCharmmFiles(unittest.TestCase): ...@@ -142,6 +142,43 @@ class TestCharmmFiles(unittest.TestCase):
diff = norm(f1-f2) diff = norm(f1-f2)
self.assertTrue(diff < 0.1 or diff/norm(f1) < 1e-4) self.assertTrue(diff < 0.1 or diff/norm(f1) < 1e-4)
def test_PermissiveRead(self):
"""Compare permissive and strict reading of Charmm parameters"""
psf = CharmmPsfFile('systems/5dhfr_cube.psf')
pdb = PDBFile('systems/5dhfr_cube.pdb')
params_strict = CharmmParameterSet('systems/par_all22_prot_with_mass.inp')
params_permissive = CharmmParameterSet('systems/par_all22_prot.inp', permissive=True)
# Box dimensions (found from bounding box)
psf.setBox(62.23*angstroms, 62.23*angstroms, 62.23*angstroms)
# Turn off charges so we only test the Lennard-Jones energies
for a in psf.atom_list:
a.charge = 0.0
# Now compute the full energy
plat = Platform.getPlatformByName('Reference')
system_strict = psf.createSystem(params_strict , nonbondedMethod=PME,
nonbondedCutoff=8*angstroms)
system_permissive = psf.createSystem(params_permissive, nonbondedMethod=PME,
nonbondedCutoff=8*angstroms)
con_strict = Context(system_strict , VerletIntegrator(2*femtoseconds), plat)
con_permissive = Context(system_permissive, VerletIntegrator(2*femtoseconds), plat)
con_strict.setPositions(pdb.positions)
con_permissive.setPositions(pdb.positions)
state_strict = con_strict.getState(getEnergy=True, enforcePeriodicBox=True)
state_permissive = con_permissive.getState(getEnergy=True, enforcePeriodicBox=True)
ene_strict = state_strict.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
ene_permissive = state_permissive.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene_strict, ene_permissive, delta=0.00001)
if __name__ == '__main__': if __name__ == '__main__':
unittest.main() unittest.main()
wrappers/python/tests/systems/5dhfr_cube.pdb 0 → 100644
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wrappers/python/tests/systems/5dhfr_cube.psf 0 → 100644
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This source diff could not be displayed because it is too large. You can view the blob instead.
wrappers/python/tests/systems/par_all22_prot.inp 0 → 100644
View file @ d1afc976
*>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<<<
*>>>>>>>>>>>>>>>>>>>>>>> July 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
*>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
*>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
*
! 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)
!
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
C C 600.000 1.3350 ! ALLOW ARO HEM
! Heme vinyl substituent (KK, from propene (JCS))
CA CA 305.000 1.3750 ! ALLOW ARO
! benzene, JES 8/25/89
CE1 CE1 440.000 1.3400 !
! for butene; from propene, yin/adm jr., 12/95
CE1 CE2 500.000 1.3420 !
! for propene, yin/adm jr., 12/95
CE1 CT2 365.000 1.5020 !
! for butene; from propene, yin/adm jr., 12/95
CE1 CT3 383.000 1.5040 !
! for butene, yin/adm jr., 12/95
CE2 CE2 510.000 1.3300 !
! for ethene, yin/adm jr., 12/95
CP1 C 250.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP1 CC 250.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP1 CD 200.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 222.500 1.5270 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP2 222.500 1.5370 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 CP2 222.500 1.5370 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CPB C 450.000 1.3800 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CPB CPA 299.800 1.4432 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB CPB 340.700 1.3464 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPH1 CPH1 410.000 1.3600 ! ALLOW ARO
! histidine, adm jr., 6/27/90
CPM CPA 360.000 1.3716 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPT CA 305.000 1.3680 ! ALLOW ARO
! adm jr., 12/30/91, for jwk
CPT CPT 360.000 1.4000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT1 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT1 CT1 222.500 1.5000 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT2 CA 230.000 1.4900 ! ALLOW ALI ARO
! phe,tyr, JES 8/25/89
CT2 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT2 CPB 230.000 1.4900 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT2 CPH1 229.630 1.5000 ! ALLOW ARO
! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
CT2 CT1 222.500 1.5380 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 CT2 222.500 1.5300 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT3 CA 230.000 1.4900 ! ALLOW ALI ARO
! toluene, adm jr. 3/7/92
CT3 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT3 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT3 CPB 230.000 1.4900 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT3 CPH1 229.630 1.5000 ! ALLOW ARO
! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
CT3 CS 190.000 1.5310 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
CT3 CT1 222.500 1.5380 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT2 222.500 1.5280 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT3 222.500 1.5300 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CY CA 350.000 1.3650 ! ALLOW ARO
!adm jr., 5/08/91, indole CCDB structure search
CY CPT 350.000 1.4400 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CY CT2 230.000 1.5100 ! ALLOW ARO
!JWK Kb from alkane freq.. b0 from TRP crystal
FE CM 258.000 1.9000 ! ALLOW HEM
! Heme (6-liganded): CO ligand (KK 05/13/91)
FE CPM 0.000 3.3814 ! ALLOW HEM
! Heme (6-liganded): for "ic para" only (KK 05/13/91)
H CD 330.000 1.1100 ! ALLOW PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA C 330.000 1.1000 ! ALLOW ARO HEM
! Heme vinyl substituent (KK, from propene (JCS))
HA CA 340.000 1.0830 ! ALLOW ARO
! trp, adm jr., 10/02/89
HA CC 317.130 1.1000 ! ALLOW POL
! adm jr., 5/13/91, formamide geometry and vibrations
HA CP2 309.000 1.1110 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 309.000 1.1110 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CPM 367.600 1.0900 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
HA CS 300.000 1.1110 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CT1 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT2 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT3 322.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CY 330.000 1.0800 ! ALLOW ARO
! JWK 05/14/91 new r0 from indole
HA1 CE1 360.500 1.1000 !
! for propene, yin/adm jr., 12/95
HA2 CE2 365.000 1.1000 !
! for ethene, yin/adm jr., 12/95
HB CP1 330.000 1.0800 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CT1 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT2 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT3 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HP CA 340.000 1.0800 ! ALLOW ARO
! phe,tyr JES 8/25/89
HP CY 350.000 1.0800 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
HR1 CPH1 375.000 1.0830 ! ALLOW ARO
! his, adm jr., 6/27/90
HR1 CPH2 340.000 1.0900 ! ALLOW ARO
! his, adm jr., 6/28/29
HR2 CPH2 333.000 1.0700 ! ALLOW ARO
! his, adm jr., 6/27/90
HR3 CPH1 365.000 1.0830 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HT HT 0.000 1.5139 ! ALLOW WAT
! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM)
N C 260.000 1.3000 ! ALLOW PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 320.000 1.4340 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP3 320.000 1.4550 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC2 C 463.000 1.3650 ! ALLOW PEP POL ARO
! 403.0->463.0, 1.305->1.365 guanidinium (KK)
NC2 CT2 261.000 1.4900 ! ALLOW ALI POL
! arg, (DS)
NC2 CT3 261.000 1.4900 ! ALLOW ALI POL
! methylguanidinium, adm jr., 3/26/92
NC2 HC 455.000 1.0000 ! ALLOW POL
! 405.0->455.0 GUANIDINIUM (KK)
NH1 C 370.000 1.3450 ! ALLOW PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 320.000 1.4300 ! ALLOW ALI PEP POL ARO
! NMA Gas & Liquid Phase IR Spectra (LK)
NH1 CT2 320.000 1.4300 ! ALLOW ALI PEP POL ARO
! NMA Gas & Liquid Phase IR Spectra (LK)
NH1 CT3 320.000 1.4300 ! ALLOW ALI PEP POL ARO
! NMA Gas & Liquid Phase IR Spectra (LK)
NH1 H 440.000 0.9970 ! ALLOW PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 HC 405.000 0.9800 ! ALLOW PEP POL ARO
! (DS)
NH2 CC 430.000 1.3600 ! ALLOW PEP POL ARO
! adm jr. 4/10/91, acetamide
NH2 CT2 240.000 1.4550
! from NH2 CT3, neutral glycine, adm jr.
NH2 CT3 240.000 1.4550 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
NH2 H 480.000 1.0000 ! ALLOW POL
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 HC 460.000 1.0000 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
NH3 CT1 200.000 1.4800 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 CT2 200.000 1.4800 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 CT3 200.000 1.4800 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 HC 403.000 1.0400 ! ALLOW POL
! new stretch and bend; methylammonium (KK 03/10/92)
NP CP1 320.000 1.4850 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP3 320.000 1.5020 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP HC 460.000 1.0060 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NPH CPA 377.200 1.3757 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH FE 270.200 1.9580 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NR1 CPH1 400.000 1.3800 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR1 CPH2 400.000 1.3600 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR1 H 466.000 1.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 CPH1 400.000 1.3800 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 CPH2 400.000 1.3200 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 FE 65.000 2.2000 ! ALLOW HEM
! Heme (6-liganded): His ligand (KK 05/13/91)
NR3 CPH1 380.000 1.3700 ! ALLOW ARO
! his, adm jr., 6/28/90
NR3 CPH2 380.000 1.3200 ! ALLOW ARO
! his, adm jr., 6/27/90
NR3 H 453.000 1.0000 ! ALLOW ARO
! his, adm jr., 6/27/90
NY CA 270.000 1.3700 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
NY CPT 270.000 1.3750 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
NY H 465.000 0.9760 ! ALLOW ARO
! indole JWK 08/28/89
O C 620.000 1.2300 ! ALLOW PEP POL ARO
! Peptide geometry, condensed phase (LK)
O CC 650.000 1.2300 ! ALLOW PEP POL ARO
! adm jr. 4/10/91, acetamide
OB CC 750.000 1.2200 ! ALLOW PEP POL ARO
! adm jr., 10/17/90, acetic acid vibrations and geom.
OB CD 750.000 1.2200 ! ALLOW PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
OC CA 525.000 1.2600 ! ALLOW PEP POL ARO ION
! adm jr. 8/27/91, phenoxide
OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION
! adm jr. 7/23/91, acetic acid
OC CT2 450.000 1.3300 ! ALLOW ALC
! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
OC CT3 450.000 1.3300 ! ALLOW ALC
! methoxide 6-31+G* geom/freq, adm jr., 6/1/92
OH1 CA 334.300 1.4110 ! ALLOW ARO ALC
! MeOH, EMB 10/10/89,
OH1 CD 230.000 1.4000 ! ALLOW PEP POL ARO ALC
! adm jr. 5/02/91, acetic acid pure solvent
OH1 CT1 428.000 1.4200 ! ALLOW ALI ALC ARO
! methanol vib fit EMB 11/21/89
OH1 CT2 428.000 1.4200 ! ALLOW ALI ALC ARO
! methanol vib fit EMB 11/21/89
OH1 CT3 428.000 1.4200 ! ALLOW ALI ALC ARO
! methanol vib fit EMB 11/21/89
OH1 H 545.000 0.9600 ! ALLOW ALC ARO
! EMB 11/21/89 methanol vib fit
OM CM 1115.000 1.1280 ! ALLOW HEM
! Heme (6-liganded): CO ligand (KK 05/13/91)
OM FE 250.000 1.8000 ! ALLOW HEM
! Heme (6-liganded): O2 ligand (KK 05/13/91)
OM OM 600.000 1.2300 ! ALLOW HEM
! Heme (6-liganded): O2 ligand (KK 05/13/91)
OS CD 150.000 1.3340 ! ALLOW POL PEP
! adm jr. 5/02/91, acetic acid pure solvent
OS CT3 340.000 1.4300 ! ALLOW POL PEP
! adm jr., 4/05/91, for PRES CT1 from methylacetate
OT HT 450.000 0.9572 ! ALLOW WAT
! FROM TIPS3P GEOM
S CT2 198.000 1.8180 ! ALLOW ALI SUL ION
! fitted to C-S s 9/26/92 (FL)
S CT3 240.000 1.8160 ! ALLOW ALI SUL ION
! fitted to C-S s 9/26/92 (FL)
S HS 275.000 1.3250 ! ALLOW SUL ION
! methanethiol pure solvent, adm jr., 6/22/92
SM CT2 214.000 1.8160 ! ALLOW SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
SM CT3 214.000 1.8160 ! ALLOW SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
SM SM 173.000 2.0290 ! ALLOW SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
SS CS 205.000 1.8360 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
ANGLES
!
!V(angle) = Ktheta(Theta - Theta0)**2
!
!V(Urey-Bradley) = Kub(S - S0)**2
!
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley)
!S0: A
!
!atom types Ktheta Theta0 Kub S0
!
CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO
! JES 8/25/89
CE1 CE1 CT3 48.00 123.50 !
! for 2-butene, yin/adm jr., 12/95
CE1 CT2 CT3 32.00 112.20 !
! for 1-butene; from propene, yin/adm jr., 12/95
CE2 CE1 CT2 48.00 126.00 !
! for 1-butene; from propene, yin/adm jr., 12/95
CE2 CE1 CT3 47.00 125.20 !
! for propene, yin/adm jr., 12/95
CP1 N C 60.000 117.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 C 52.000 112.3000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 CC 52.000 112.3000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 CD 50.000 112.3000 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP2 CP1 70.000 108.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 CP2 CP2 70.000 108.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 N C 60.000 117.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 N CP1 100.000 114.2000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 NP CP1 100.000 111.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CPA CPB C 70.000 126.7400 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CPA CPM CPA 94.200 125.1200 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPA NPH CPA 139.300 103.9000 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB C C 70.000 121.5000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CPB CPB C 70.000 126.7500 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CPB CPB CPA 30.800 106.5100 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPH2 NR1 CPH1 130.000 107.5000 ! ALLOW ARO
! his, adm jr., 6/27/90
CPH2 NR2 CPH1 130.000 104.0000 ! ALLOW ARO
! his, adm jr., 6/27/90
CPH2 NR3 CPH1 145.000 108.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
CPM CPA CPB 61.600 124.0700 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPT CA CA 60.000 118.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CPT CPT CA 60.000 122.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CPT CY CA 120.000 107.40 25.00 2.26100 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CPT NY CA 110.000 108.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CT1 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
CT1 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT1 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO
! PARALLH19 (JES)
CT1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
CT1 CT2 CPH1 58.350 113.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted
CT1 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT1 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
CT2 CA CA 45.800 122.3000 ! ALLOW ALI ARO
! PARALLH19 (JES)
CT2 CPB CPA 65.000 126.7400 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT2 CPB CPB 65.000 126.7500 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT2 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS
CT2 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
CT2 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
CT2 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 CT2 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! from CT2 CT1 C, for lactams, adm jr.
CT2 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
CT2 CT2 CPB 70.000 113.0000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT2 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT2 CT2 CT2 58.350 113.60 11.16 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 CT3 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT2 CY CA 45.800 129.4000 ! ALLOW ARO
!adm jr., 5/08/91, indole CCDB structure search
CT2 CY CPT 45.800 124.0000 ! ALLOW ARO
!adm jr., 5/08/91, indole CCDB structure search
CT2 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO
! 107.5->120.0 to make planar Arg (KK)
CT2 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
CT2 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP
! adm jr. 5/02/91, acetic acid pure solvent
CT3 CA CA 45.800 122.3000 ! ALLOW ALI ARO
! toluene, adm jr., 3/7/92
CT3 CPB CPA 65.000 126.7400 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT3 CPB CPB 65.000 126.7500 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT3 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS
CT3 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/09/92, for ALA cter
CT3 CT1 CT1 53.350 108.50 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT1 CT2 53.350 114.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT1 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO
! ethylbenzene, adm jr., 3/7/92
CT3 CT2 CPH1 58.350 113.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted
CT3 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT3 CT2 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT2 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO
! methylguanidinium, adm jr., 3/26/92
CT3 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
CT3 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP
! adm jr. 5/02/91, acetic acid pure solvent
CT3 S CT2 34.000 95.0000 ! ALLOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
CY CPT CA 160.000 130.6000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CY CPT CPT 110.000 107.4000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CY CT2 CT1 58.350 114.0000 ! ALLOW ARO
! from TRP crystal, JWK
CY CT2 CT3 58.350 114.0000 ! ALLOW ARO
! from TRP crystal, JWK
FE NPH CPA 96.150 128.0500 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
FE NR2 CPH1 30.000 133.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
FE NR2 CPH2 30.000 123.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
H NH1 C 34.000 123.0000 ! ALLOW PEP POL ARO
! NMA Vib Modes (LK)
H NH1 CT1 35.000 117.0000 ! ALLOW PEP POL ARO ALI
! NMA Vibrational Modes (LK)
H NH1 CT2 35.000 117.0000 ! ALLOW PEP POL ARO ALI
! NMA Vibrational Modes (LK)
H NH1 CT3 35.000 117.0000 ! ALLOW PEP POL ARO ALI
! NMA Vibrational Modes (LK)
H NH2 CC 50.000 120.0000 ! ALLOW POL PEP ARO
! his, adm jr. 8/13/90 acetamide geometry and vibrations
H NH2 H 23.000 120.0000 ! ALLOW POL
! adm jr. 8/13/90 acetamide geometry and vibrations
H NR1 CPH1 30.000 125.50 20.00 2.15000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NR1 CPH2 30.000 127.00 20.00 2.14000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NR3 CPH1 25.000 126.00 15.00 2.13000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NR3 CPH2 25.000 126.00 15.00 2.09000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NY CA 28.000 126.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
H NY CPT 28.000 126.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
H OH1 CA 65.000 108.0000 ! ALLOW ALC ARO
! JES 8/25/89 phenol
H OH1 CD 55.000 115.0000 ! ALLOW ALC ARO PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
H OH1 CT1 57.500 106.0000 ! ALLOW ALC ARO ALI
! methanol vib fit EMB 11/21/89
H OH1 CT2 57.500 106.0000 ! ALLOW ALC ARO ALI
! methanol vib fit EMB 11/21/89
H OH1 CT3 57.500 106.0000 ! ALLOW ALC ARO ALI
! methanol vib fit EMB 11/21/89
HA C C 50.000 120.5000 ! ALLOW PEP POL ARO
! Heme vinyl substituent (KK from propene (JCS))
HA C CPB 50.000 120.0000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
HA C HA 50.000 118.0000 ! ALLOW PEP POL ARO
! Heme vinyl substituent (KK from propene (JCS))
HA CA CA 29.000 120.00 25.00 2.15250 ! ALLOW ARO
! trp, adm jr., 10/02/89
HA CA CPT 41.000 122.0000 ! ALLOW ARO
!adm jr., 5/08/91, indole CCDB structure search
HA CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HA CP2 CP1 33.430 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP2 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP2 CP3 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CPM CPA 12.700 117.4400 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
HA CPM FE 0.000 180.0000 ! ALLOW HEM
! Heme (6-liganded): for "ic para" only (KK 05/13/91)
HA CS CT3 34.600 110.10 22.53 2.17900 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CS HA 35.500 108.40 14.00 1.77500 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CT1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA CT1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA CT1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT1 HA 35.500 109.00 5.40 1.80200 ! TEST for test cpd
! based on HA CT2 HA
HA CT2 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA CT2 CA 49.300 107.5000 ! ALLOW ALI ARO
! PARALLH19 (JES)
HA CT2 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HA CT2 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA CT2 CE1 45.00 111.50 !
! for 1-butene; from propene, yin/adm jr., 12/95
HA CT2 CPB 50.000 109.5000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
HA CT2 CPH1 33.430 109.5000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
HA CT2 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
HA CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT2 CY 33.430 109.5000 ! ALLOW ARO
! ADM JR., 10/02/89, from CT2CT2HA (U-B OMITTED), FOR JOANNA
HA CT2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT3 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA CT3 CA 49.300 107.5000 ! ALLOW ALI ARO
! toluene, adm jr. 3/7/92
HA CT3 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HA CT3 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA CT3 CE1 42.00 111.50 !
! for 2-butene, yin/adm jr., 12/95
HA CT3 CPB 50.000 109.5000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
HA CT3 CPH1 33.430 109.5000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
HA CT3 CS 34.600 110.10 22.53 2.17900 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
HA CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CY CA 20.000 126.40 25.00 2.18600 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HA CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HA1 CE1 CE1 52.00 119.50 !
! for 2-butene, yin/adm jr., 12/95
HA1 CE1 CE2 42.00 118.00 !
! for propene, yin/adm jr., 12/95
HA1 CE1 CT2 40.00 116.00 !
! for 1-butene; from propene, yin/adm jr., 12/95
HA1 CE1 CT3 22.00 117.00 !
! for propene, yin/adm jr., 12/95
HA2 CE2 CE1 45.00 120.50 !
! for propene, yin/adm jr., 12/95
HA2 CE2 CE2 55.50 120.50 !
! for ethene, yin/adm jr., 12/95
HA2 CE2 HA2 19.00 119.00 !
! for propene, yin/adm jr., 12/95
HB CP1 C 50.000 112.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CP1 CC 50.000 112.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CP1 CD 50.000 112.0000 ! ALLOW PEP POL PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CP1 CP2 35.000 118.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CT1 C 50.000 109.5000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT1 CC 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HB CT1 CD 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
HB CT1 CT1 35.000 111.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT1 CT2 35.000 111.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT1 CT3 35.000 111.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT2 C 50.000 109.5000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT2 CC 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HB CT2 CD 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
HB CT2 HB 36.000 115.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT3 C 50.000 109.5000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HC NC2 C 49.000 120.0000 ! ALLOW POL PEP ARO
! 35.3->49.0 GUANIDINIUM (KK)
HC NC2 CT2 40.400 120.0000 ! ALLOW POL ALI
! 107.5->120.0 to make planar Arg (KK)
HC NC2 CT3 40.400 120.0000 ! ALLOW POL ALI
! methylguanidinium, adm jr., 3/26/92
HC NC2 HC 25.000 120.0000 ! ALLOW POL
! 40.0->25.0 GUANIDINIUM (KK)
HC NH2 CT2 50.000 111.0000 ! ALLOW POL
! from HC NH2 CT3, neutral glycine, adm jr.
HC NH2 CT3 50.000 111.0000 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
HC NH2 HC 39.000 106.5000 ! ALLOW POL
! 40.0->25.0 GUANIDINIUM (KK)
HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
! new stretch and bend; methylammonium (KK 03/10/92)
HC NH3 CT2 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
! new stretch and bend; methylammonium (KK 03/10/92)
HC NH3 CT3 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
! new stretch and bend; methylammonium (KK 03/10/92)
HC NH3 HC 44.000 109.5000 ! ALLOW POL
! new stretch and bend; methylammonium (KK 03/10/92)
HC NP CP1 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HC NP CP3 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HC NP HC 51.000 107.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HP CA CA 30.000 120.00 22.00 2.15250 ! ALLOW ARO
! JES 8/25/89 benzene
HP CA CPT 30.000 122.00 22.00 2.14600 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
HP CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HP CY CA 32.000 126.40 25.00 2.18600 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
HP CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HR1 CPH1 CPH1 22.000 130.00 15.00 2.21500 ! ALLOW ARO
! adm jr., 6/27/90, his
HR3 CPH1 CPH1 25.000 130.00 20.00 2.20000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HS S CT2 38.800 95.0000 ! ALLOW SUL ION ALI
! methanethiol pure solvent, adm jr., 6/22/92
HS S CT3 43.000 95.0000 ! ALLOW SUL ION ALI
! methanethiol pure solvent, adm jr., 6/22/92
HT OT HT 55.000 104.5200 ! ALLOW WAT
! TIP3P GEOMETRY, ADM JR.
N C CP1 20.000 112.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT1 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT2 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT3 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 C 50.000 108.2000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 CC 50.000 108.2000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 CD 50.000 108.2000 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 CP2 70.000 110.8000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 HB 48.000 112.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP3 CP2 70.000 110.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP3 HA 48.000 108.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC2 C NC2 52.000 120.00 90.00 2.36420 ! ALLOW POL PEP ARO
! changed from 60.0/120.3 for guanidinium (KK)
NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL
! arg, (DS)
NC2 CT2 HA 51.500 107.5000 ! ALLOW ALI POL
! arg, (DS)
NC2 CT3 HA 51.500 107.5000 ! ALLOW ALI POL
! methylguanidinium, adm jr., 3/26/92
NH1 C CP1 80.000 116.5000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH1 C CT1 80.000 116.5000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
NH1 C CT2 80.000 116.5000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
NH1 C CT3 80.000 116.5000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
NH1 CT1 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
NH1 CT1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 5/02/91, acetic acid pure solvent
NH1 CT1 CT1 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 HB 48.000 108.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT2 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT2 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 5/20/92, for asn,asp,gln,glu and cters
NH1 CT2 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 5/02/91, acetic acid pure solvent
NH1 CT2 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! from NH1 CT1 CT2, for lactams, adm jr.
NH1 CT2 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO
! from NH1 CT3 HA, for lactams, adm jr.
NH1 CT2 HB 48.000 108.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT3 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO
! NMA crystal (JCS)
NH2 CC CP1 80.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH2 CC CT1 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 CC CT3 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 CC HA 44.000 111.00 50.00 1.98000 ! ALLOW POL
! adm jr., 5/13/91, formamide geometry and vibrations
NH2 CT2 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
! 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
! adm jr. 4/10/91, acetamide update
OB CD CP1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
OB CD CT1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
OB CD CT2 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
OB CD CT3 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
OC CA CA 40.000 120.0000 ! ALLOW POL ARO
! adm jr. 8/27/91, phenoxide
OC CC CP1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION
! adm jr. 7/23/91, correction, ACETATE (KK)
OC CC CT2 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION
! adm jr. 7/23/91, correction, ACETATE (KK)
OC CC CT3 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION
! adm jr. 7/23/91, correction, ACETATE (KK)
OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO
! adm jr. 7/23/91, correction, ACETATE (KK)
OC CT2 CT3 65.000 122.0000 ! ALLOW ALC
! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
OC CT2 HA 65.000 118.3000 ! ALLOW ALC
! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
OC CT3 HA 65.000 118.3000 ! ALLOW ALC
! methoxide 6-31+G* geom/freq, adm jr., 6/1/92
OH1 CA CA 45.200 120.0000 ! ALLOW ARO ALC
! PARALLH19 WITH [122.3] (JES)
OH1 CD CT2 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC
! adm jr, 10/17/90, acetic acid vibrations
OH1 CD CT3 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC
! adm jr, 10/17/90, acetic acid vibrations
OH1 CD OB 50.000 123.00 210.00 2.26200 ! ALLOW PEP POL ARO ALC
! adm jr, 10/17/90, acetic acid vibrations
OH1 CT1 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT1 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT1 HA 45.900 108.8900 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT2 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT2 CT2 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT2 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT2 HA 45.900 108.8900 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT3 HA 45.900 108.8900 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OM CM FE 35.000 180.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
OM FE NPH 5.000 90.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
OM OM FE 0.000 180.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
OS CD CP1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
OS CD CT1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP
! adm jr., 4/05/91, for PRES CT1 from methylacetate
OS CD CT2 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP
! adm jr., 4/05/91, for PRES CT1 from methylacetate
OS CD CT3 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP
! adm jr., 4/05/91, for PRES CT1 from methylacetate
OS CD OB 90.000 125.90 160.00 2.25760 ! ALLOW PEP POL
! adm jr. 3/19/92, from lipid methyl acetate
OS CT2 HA 60.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for PRES CT1 from methyl acetate
OS CT3 HA 60.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for PRES CT1 from methyl acetate
S CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION
! as in expt.MeEtS & DALC crystal, 5/15/92
S CT2 CT2 58.000 114.5000 ! ALLOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
S CT2 CT3 58.000 114.5000 ! ALLOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
S CT2 HA 46.100 111.3000 ! ALLOW ALI SUL ION
! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90
S CT3 HA 46.100 111.3000 ! ALLOW ALI SUL ION
! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90
SM CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION
! as in expt.MeEtS & DALC crystal, 5/15/92
SM CT2 HA 38.000 111.0000 ! ALLOW ALI SUL ION
! new S-S atom type 8/24/90
SM CT3 HA 38.000 111.0000 ! ALLOW ALI SUL ION
! new S-S atom type 8/24/90
SM SM CT2 72.500 103.3000 ! ALLOW ALI SUL ION
! expt. dimethyldisulfide, 3/26/92 (FL)
SM SM CT3 72.500 103.3000 ! ALLOW ALI SUL ION
! expt. dimethyldisulfide, 3/26/92 (FL)
SS CS CT3 55.000 118.0000 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
SS CS HA 40.000 112.3000 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types Kchi n delta
!
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 HA2 5.2000 2 180.00 !
! for propene, yin/adm jr., 12/95
CT3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO
! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2
CT3 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP
! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
CT3 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI
! ethylbenzene ethyl rotation, adm jr. 3/7/92
CT3 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO
! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CT3 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO
! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CT3 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CT3 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI
! alkane update, adm jr., 3/2/92, butane trans/gauche
CT3 CT2 CT2 CT3 0.1500 1 0.00 ! ALLOW ALI
! alkane update, adm jr., 3/2/92, butane trans/gauche
CT3 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO
! from ethylbenzene, adm jr., 3/7/92
CT3 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO
! from ethylbenzene, adm jr., 3/7/92
CT3 CT2 S CT3 0.2400 1 180.00 ! ALOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
CT3 CT2 S CT3 0.3700 3 0.00 ! ALOW ALI SUL ION
! DTN 8/24/90
CT3 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT3 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT3 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP
! Revised to adjust NMA cis/trans energy difference. (LK)
CT3 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
CT3 S CT2 CT2 0.2400 1 180.00 ! ALOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
CT3 S CT2 CT2 0.3700 3 0.00 ! ALOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
CT3 SM SM CT3 1.0000 1 0.00 ! ALLOW ALI SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
CT3 SM SM CT3 4.1000 2 0.00 ! ALLOW ALI SUL ION
! mp 6-311G** dimethyldisulfide, 3/26/92 (FL)
CT3 SM SM CT3 0.9000 3 0.00 ! ALLOW ALI SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
CY CA NY CPT 5.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
CY CPT CA CA 3.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
CY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
H NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
H NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
H NH1 C CT2 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
H NH1 C CT3 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
H NH1 CT1 C 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
H NH1 CT1 CC 0.0000 1 0.00 ! ALLOW PEP POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
H NH1 CT1 CD 0.0000 1 0.00 ! ALLOW PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
H NH1 CT1 CT1 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
H NH1 CT1 CT2 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
H NH1 CT1 CT3 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
H NH1 CT2 C 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
H NH1 CT2 CC 0.0000 1 0.00 ! ALLOW PEP POL
! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
H NH1 CT2 CD 0.0000 1 0.00 ! ALLOW PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
H NH1 CT2 CT2 0.0000 1 0.00 ! ALLOW PEP
! from H NH1 CT2 CT3, for lactams, adm jr.
H NH1 CT2 CT3 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
H NH2 CC CT1 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
! adm jr. 4/10/91, acetamide update
H NH2 CC CT2 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
! adm jr. 4/10/91, acetamide update
H NH2 CC CT3 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
! adm jr. 4/10/91, acetamide update
H NH2 CC CP1 2.5000 2 180.00 ! ALLOW PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
H NR1 CPH1 CPH1 1.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 7/20/89
H NR1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H
H NR1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H
H NR3 CPH1 CPH1 1.4000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90
H NR3 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA
H NR3 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA
H NY CA CY 0.8000 2 180.00 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
H NY CPT CA 0.8000 2 180.00 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
H NY CPT CPT 0.8000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
H OH1 CA CA 0.9900 2 180.00 ! ALLOW ARO ALC
! phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92
H OH1 CT1 CT1 1.3300 1 0.00 ! ALLOW ALC
! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT1 CT1 0.1800 2 0.00 ! ALLOW ALC
! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT1 CT1 0.3200 3 0.00 ! ALLOW ALC
! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT1 CT3 1.3300 1 0.00 ! ALLOW ALC
! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT1 CT3 0.1800 2 0.00 ! ALLOW ALC
! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT1 CT3 0.3200 3 0.00 ! ALLOW ALC
! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT1 1.3000 1 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT1 0.3000 2 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT1 0.4200 3 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT2 1.3000 1 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT2 0.3000 2 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT2 0.4200 3 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT3 1.3000 1 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT3 0.3000 2 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT3 0.4200 3 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
HA CA CA CA 3.5000 2 180.00 ! ALLOW ARO
! adm jr., 10/02/89
HA CA CA CPT 3.5000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CA CA HA 2.5000 2 180.00 ! ALLOW ARO
! ADM JR., 10/02/89
HA CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO
! TRP (JES)
HA CA CPT CY 4.0000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CA CY CPT 1.2000 2 180.00 ! ALLOW ARO
! JWK
HA CA CY CT2 1.2000 2 180.00 ! ALLOW ARO
! JWK
HA CA NY CPT 3.0000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CA NY H 1.0000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL
! adm jr. 4/10/91, acetamide update
HA CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
HA CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89
HA CT2 CY CA 0.2500 2 180.00 ! ALLOW ARO
! JWK
HA CT2 CY CPT 0.2500 2 180.00 ! ALLOW ARO
! JWK
HA CT2 NH1 C 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
HA CT2 NH1 H 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
HA CT2 S CT3 0.2800 3 0.00 ! ALLOW ALI SUL ION
! DTN 8/24/90
HA CT3 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89
HA CT3 CS HA 0.1600 3 0.00 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CT3 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
HA CT3 NH1 C 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
HA CT3 NH1 H 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
HA CT3 S CT2 0.2800 3 0.00 ! ALLOW ALI SUL ION
! DTN 8/24/90
HA CY CA CPT 1.2000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CY CA HA 1.2000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA1 CE1 CE2 HA2 5.2000 2 180.00 !
! for propene, yin/adm jr., 12/95
HA1 CE1 CT2 HA 0.8700 3 0.00 !
! for butene, yin/adm jr., 12/95
HA1 CE1 CT2 CT3 0.1200 3 0.00 !
! for butene, yin/adm jr., 12/95
HA1 CE1 CT3 HA 0.3400 3 0.00 !
! for butene, yin/adm jr., 12/95
HA2 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)
IMPROPER
!
!V(improper) = Kpsi(psi - psi0)**2
!
!Kpsi: kcal/mole/rad**2
!psi0: degrees
!note that the second column of numbers (0) is ignored
!
!atom types Kpsi psi0
!
CPB CPA NPH CPA 20.8000 0 0.0000 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB X X 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))
HA2 HA2 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)
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
!
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
HA1 0.000000 -0.031000 1.250000 !
! for propene, yin/adm jr., 12/95
HA2 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
!HA1 0.000000 -0.031000 1.250000
!HA2 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
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
wrappers/python/tests/systems/par_all22_prot_with_mass.inp 0 → 100644
View file @ d1afc976
*>>>> CHARMM22 All-Hydrogen Parameter File for Proteins <<<<<<<<<<
*>>>>>>>>>>>>>>>>>>>>>>> July 1997 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
*>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
*>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
*
! 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)
!
ATOMS
MASS 1 H 1.00800 H ! polar H
MASS 2 HC 1.00800 H ! N-ter H
MASS 3 HA 1.00800 H ! nonpolar H
MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN
MASS 5 HP 1.00800 H ! aromatic H
MASS 6 HB 1.00800 H ! backbone H
MASS 7 HR1 1.00800 H ! his he1, (+) his HG,HD2
MASS 8 HR2 1.00800 H ! (+) his HE1
MASS 9 HR3 1.00800 H ! neutral his HG, HD2
MASS 10 HS 1.00800 H ! thiol hydrogen
MASS 11 HE1 1.00800 H ! for alkene; RHC=CR
MASS 12 HE2 1.00800 H ! for alkene; H2C=CR
MASS 13 HA1 1.00800 H ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS 14 HA2 1.00800 H ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS 15 HA3 1.00800 H ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS 16 HF1 1.00800 H ! Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str)
MASS 17 HF2 1.00800 H ! Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str)
MASS 20 C 12.01100 C ! carbonyl C, peptide backbone
MASS 21 CA 12.01100 C ! aromatic C
MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH
MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2
MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3
MASS 25 CPH1 12.01100 C ! his CG and CD2 carbons
MASS 26 CPH2 12.01100 C ! his CE1 carbon
MASS 27 CPT 12.01100 C ! trp C between rings
MASS 28 CY 12.01100 C ! TRP C in pyrrole ring
MASS 29 CP1 12.01100 C ! tetrahedral C (proline CA)
MASS 30 CP2 12.01100 C ! tetrahedral C (proline CB/CG)
MASS 31 CP3 12.01100 C ! tetrahedral C (proline CD)
MASS 32 CC 12.01100 C ! carbonyl C, asn,asp,gln,glu,cter,ct2
MASS 33 CD 12.01100 C ! carbonyl C, pres aspp,glup,ct1
MASS 34 CPA 12.01100 C ! heme alpha-C
MASS 35 CPB 12.01100 C ! heme beta-C
MASS 36 CPM 12.01100 C ! heme meso-C
MASS 37 CM 12.01100 C ! heme CO carbon
MASS 38 CS 12.01100 C ! thiolate carbon
MASS 39 CE1 12.01100 C ! for alkene; RHC=CR
MASS 40 CE2 12.01100 C ! for alkene; H2C=CR
MASS 41 CST 12.01100 C ! CO2 carbon
MASS 42 CT 12.01100 C ! aliphatic sp3 C, new LJ params, no hydrogens (see toppar_all22_prot_aliphatic_c27.str)
MASS 43 CT1x 12.01100 C ! aliphatic sp3 C for CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS 44 CT2x 12.01100 C ! aliphatic sp3 C for CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS 45 CT3x 12.01100 C ! aliphatic sp3 C for CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS 46 CN 12.01100 C ! C for cyano group (see toppar_all22_prot_pyridines.str)
MASS 47 CAP 12.01100 C ! aromatic C for pyrimidines (see toppar_all22_prot_pyridines.str)
MASS 48 COA 12.01100 C ! carbonyl C for pyrimidines (see toppar_all22_prot_pyridines.str)
MASS 49 C3 12.01100 C ! cyclopropyl carbon
MASS 50 N 14.00700 N ! proline N
MASS 51 NR1 14.00700 N ! neutral his protonated ring nitrogen
MASS 52 NR2 14.00700 N ! neutral his unprotonated ring nitrogen
MASS 53 NR3 14.00700 N ! charged his ring nitrogen
MASS 54 NH1 14.00700 N ! peptide nitrogen
MASS 55 NH2 14.00700 N ! amide nitrogen
MASS 56 NH3 14.00700 N ! ammonium nitrogen
MASS 57 NC2 14.00700 N ! guanidinium nitroogen
MASS 58 NY 14.00700 N ! TRP N in pyrrole ring
MASS 59 NP 14.00700 N ! Proline ring NH2+ (N-terminal)
MASS 60 NPH 14.00700 N ! heme pyrrole N
MASS 61 NC 14.00700 N ! N for cyano group (see toppar_all22_prot_pyridines.str)
MASS 70 O 15.99900 O ! carbonyl oxygen
MASS 71 OB 15.99900 O ! carbonyl oxygen in acetic acid
MASS 72 OC 15.99900 O ! carboxylate oxygen
MASS 73 OH1 15.99900 O ! hydroxyl oxygen
MASS 74 OS 15.99940 O ! ester oxygen
MASS 75 OT 15.99940 O ! TIPS3P WATER OXYGEN
MASS 76 OM 15.99900 O ! heme CO/O2 oxygen
MASS 77 OST 15.99900 O ! CO2 oxygen
MASS 78 OCA 15.99900 O ! carbonyl O for pyrimidines (see toppar_all22_prot_pyridines.str)
MASS 81 S 32.06000 S ! sulphur
MASS 82 SM 32.06000 S ! sulfur C-S-S-C type
MASS 83 SS 32.06000 S ! thiolate sulfur
MASS 85 HE 4.00260 HE ! helium
MASS 86 NE 20.17970 NE ! neon
MASS 87 CF1 12.01100 C ! monofluoromethyl (see toppar_all22_prot_fluoro_alkanes.str)
MASS 88 CF2 12.01100 C ! difluoromethyl (see toppar_all22_prot_fluoro_alkanes.str)
MASS 89 CF3 12.01100 C ! trifluoromethyl (see toppar_all22_prot_fluoro_alkanes.str)
MASS 90 FE 55.84700 Fe ! heme iron 56
MASS 91 CLAL 35.45300 CL ! Chlorine Atom (see toppar_all22_prot_aldehydes.str)
MASS 92 FA 18.99800 F ! aromatic flourine (see toppar_all22_prot_pyridines.str)
MASS 93 F1 18.99800 F ! Fluorine, monofluoro (see toppar_all22_prot_fluoro_alkanes.str)
MASS 94 F2 18.99800 F ! Fluorine, difluoro (see toppar_all22_prot_fluoro_alkanes.str)
MASS 95 F3 18.99800 F ! Fluorine, trifluoro (see toppar_all22_prot_fluoro_alkanes.str)
MASS 99 DUM 0.00000 H ! dummy atom
MASS 100 SOD 22.989770 NA ! Sodium Ion
MASS 101 MG 24.305000 MG ! Magnesium Ion
MASS 102 POT 39.102000 K ! Potassium Ion! check masses
MASS 103 CES 132.900000 CS ! Cesium Ion
MASS 104 CAL 40.080000 CA ! Calcium Ion
MASS 105 CLA 35.450000 CL ! Chloride Ion
MASS 106 ZN 65.370000 ZN ! zinc (II) cation
MASS 112 CC1A 12.01100 C ! alkene conjugation
MASS 113 CC1B 12.01100 C ! alkene conjugation
MASS 114 CC2 12.01100 C ! alkene conjugation
MASS 120 NS1 14.00700 N ! N for deprotonated Schiff's base
MASS 121 NS2 14.00700 N ! N for protonated Schiff's base
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
C C 600.000 1.3350 ! ALLOW ARO HEM
! Heme vinyl substituent (KK, from propene (JCS))
CA CA 305.000 1.3750 ! ALLOW ARO
! benzene, JES 8/25/89
CE1 CE1 440.000 1.3400 !
! for butene; from propene, yin/adm jr., 12/95
CE1 CE2 500.000 1.3420 !
! for propene, yin/adm jr., 12/95
CE1 CT2 365.000 1.5020 !
! for butene; from propene, yin/adm jr., 12/95
CE1 CT3 383.000 1.5040 !
! for butene, yin/adm jr., 12/95
CE2 CE2 510.000 1.3300 !
! for ethene, yin/adm jr., 12/95
CP1 C 250.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP1 CC 250.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP1 CD 200.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 222.500 1.5270 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP2 222.500 1.5370 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 CP2 222.500 1.5370 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CPB C 450.000 1.3800 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CPB CPA 299.800 1.4432 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB CPB 340.700 1.3464 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPH1 CPH1 410.000 1.3600 ! ALLOW ARO
! histidine, adm jr., 6/27/90
CPM CPA 360.000 1.3716 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPT CA 305.000 1.3680 ! ALLOW ARO
! adm jr., 12/30/91, for jwk
CPT CPT 360.000 1.4000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT1 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT1 CT1 222.500 1.5000 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT2 CA 230.000 1.4900 ! ALLOW ALI ARO
! phe,tyr, JES 8/25/89
CT2 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT2 CPB 230.000 1.4900 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT2 CPH1 229.630 1.5000 ! ALLOW ARO
! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
CT2 CT1 222.500 1.5380 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 CT2 222.500 1.5300 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT3 CA 230.000 1.4900 ! ALLOW ALI ARO
! toluene, adm jr. 3/7/92
CT3 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT3 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT3 CPB 230.000 1.4900 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT3 CPH1 229.630 1.5000 ! ALLOW ARO
! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
CT3 CS 190.000 1.5310 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
CT3 CT1 222.500 1.5380 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT2 222.500 1.5280 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT3 222.500 1.5300 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CY CA 350.000 1.3650 ! ALLOW ARO
!adm jr., 5/08/91, indole CCDB structure search
CY CPT 350.000 1.4400 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CY CT2 230.000 1.5100 ! ALLOW ARO
!JWK Kb from alkane freq.. b0 from TRP crystal
FE CM 258.000 1.9000 ! ALLOW HEM
! Heme (6-liganded): CO ligand (KK 05/13/91)
FE CPM 0.000 3.3814 ! ALLOW HEM
! Heme (6-liganded): for "ic para" only (KK 05/13/91)
H CD 330.000 1.1100 ! ALLOW PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA C 330.000 1.1000 ! ALLOW ARO HEM
! Heme vinyl substituent (KK, from propene (JCS))
HA CA 340.000 1.0830 ! ALLOW ARO
! trp, adm jr., 10/02/89
HA CC 317.130 1.1000 ! ALLOW POL
! adm jr., 5/13/91, formamide geometry and vibrations
HA CP2 309.000 1.1110 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 309.000 1.1110 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CPM 367.600 1.0900 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
HA CS 300.000 1.1110 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CT1 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT2 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT3 322.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CY 330.000 1.0800 ! ALLOW ARO
! JWK 05/14/91 new r0 from indole
HA1 CE1 360.500 1.1000 !
! for propene, yin/adm jr., 12/95
HA2 CE2 365.000 1.1000 !
! for ethene, yin/adm jr., 12/95
HB CP1 330.000 1.0800 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CT1 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT2 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT3 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HP CA 340.000 1.0800 ! ALLOW ARO
! phe,tyr JES 8/25/89
HP CY 350.000 1.0800 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
HR1 CPH1 375.000 1.0830 ! ALLOW ARO
! his, adm jr., 6/27/90
HR1 CPH2 340.000 1.0900 ! ALLOW ARO
! his, adm jr., 6/28/29
HR2 CPH2 333.000 1.0700 ! ALLOW ARO
! his, adm jr., 6/27/90
HR3 CPH1 365.000 1.0830 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HT HT 0.000 1.5139 ! ALLOW WAT
! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM)
N C 260.000 1.3000 ! ALLOW PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 320.000 1.4340 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP3 320.000 1.4550 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC2 C 463.000 1.3650 ! ALLOW PEP POL ARO
! 403.0->463.0, 1.305->1.365 guanidinium (KK)
NC2 CT2 261.000 1.4900 ! ALLOW ALI POL
! arg, (DS)
NC2 CT3 261.000 1.4900 ! ALLOW ALI POL
! methylguanidinium, adm jr., 3/26/92
NC2 HC 455.000 1.0000 ! ALLOW POL
! 405.0->455.0 GUANIDINIUM (KK)
NH1 C 370.000 1.3450 ! ALLOW PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 320.000 1.4300 ! ALLOW ALI PEP POL ARO
! NMA Gas & Liquid Phase IR Spectra (LK)
NH1 CT2 320.000 1.4300 ! ALLOW ALI PEP POL ARO
! NMA Gas & Liquid Phase IR Spectra (LK)
NH1 CT3 320.000 1.4300 ! ALLOW ALI PEP POL ARO
! NMA Gas & Liquid Phase IR Spectra (LK)
NH1 H 440.000 0.9970 ! ALLOW PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 HC 405.000 0.9800 ! ALLOW PEP POL ARO
! (DS)
NH2 CC 430.000 1.3600 ! ALLOW PEP POL ARO
! adm jr. 4/10/91, acetamide
NH2 CT2 240.000 1.4550
! from NH2 CT3, neutral glycine, adm jr.
NH2 CT3 240.000 1.4550 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
NH2 H 480.000 1.0000 ! ALLOW POL
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 HC 460.000 1.0000 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
NH3 CT1 200.000 1.4800 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 CT2 200.000 1.4800 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 CT3 200.000 1.4800 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 HC 403.000 1.0400 ! ALLOW POL
! new stretch and bend; methylammonium (KK 03/10/92)
NP CP1 320.000 1.4850 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP3 320.000 1.5020 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP HC 460.000 1.0060 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NPH CPA 377.200 1.3757 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NPH FE 270.200 1.9580 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
NR1 CPH1 400.000 1.3800 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR1 CPH2 400.000 1.3600 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR1 H 466.000 1.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 CPH1 400.000 1.3800 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 CPH2 400.000 1.3200 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 FE 65.000 2.2000 ! ALLOW HEM
! Heme (6-liganded): His ligand (KK 05/13/91)
NR3 CPH1 380.000 1.3700 ! ALLOW ARO
! his, adm jr., 6/28/90
NR3 CPH2 380.000 1.3200 ! ALLOW ARO
! his, adm jr., 6/27/90
NR3 H 453.000 1.0000 ! ALLOW ARO
! his, adm jr., 6/27/90
NY CA 270.000 1.3700 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
NY CPT 270.000 1.3750 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
NY H 465.000 0.9760 ! ALLOW ARO
! indole JWK 08/28/89
O C 620.000 1.2300 ! ALLOW PEP POL ARO
! Peptide geometry, condensed phase (LK)
O CC 650.000 1.2300 ! ALLOW PEP POL ARO
! adm jr. 4/10/91, acetamide
OB CC 750.000 1.2200 ! ALLOW PEP POL ARO
! adm jr., 10/17/90, acetic acid vibrations and geom.
OB CD 750.000 1.2200 ! ALLOW PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
OC CA 525.000 1.2600 ! ALLOW PEP POL ARO ION
! adm jr. 8/27/91, phenoxide
OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION
! adm jr. 7/23/91, acetic acid
OC CT2 450.000 1.3300 ! ALLOW ALC
! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
OC CT3 450.000 1.3300 ! ALLOW ALC
! methoxide 6-31+G* geom/freq, adm jr., 6/1/92
OH1 CA 334.300 1.4110 ! ALLOW ARO ALC
! MeOH, EMB 10/10/89,
OH1 CD 230.000 1.4000 ! ALLOW PEP POL ARO ALC
! adm jr. 5/02/91, acetic acid pure solvent
OH1 CT1 428.000 1.4200 ! ALLOW ALI ALC ARO
! methanol vib fit EMB 11/21/89
OH1 CT2 428.000 1.4200 ! ALLOW ALI ALC ARO
! methanol vib fit EMB 11/21/89
OH1 CT3 428.000 1.4200 ! ALLOW ALI ALC ARO
! methanol vib fit EMB 11/21/89
OH1 H 545.000 0.9600 ! ALLOW ALC ARO
! EMB 11/21/89 methanol vib fit
OM CM 1115.000 1.1280 ! ALLOW HEM
! Heme (6-liganded): CO ligand (KK 05/13/91)
OM FE 250.000 1.8000 ! ALLOW HEM
! Heme (6-liganded): O2 ligand (KK 05/13/91)
OM OM 600.000 1.2300 ! ALLOW HEM
! Heme (6-liganded): O2 ligand (KK 05/13/91)
OS CD 150.000 1.3340 ! ALLOW POL PEP
! adm jr. 5/02/91, acetic acid pure solvent
OS CT3 340.000 1.4300 ! ALLOW POL PEP
! adm jr., 4/05/91, for PRES CT1 from methylacetate
OT HT 450.000 0.9572 ! ALLOW WAT
! FROM TIPS3P GEOM
S CT2 198.000 1.8180 ! ALLOW ALI SUL ION
! fitted to C-S s 9/26/92 (FL)
S CT3 240.000 1.8160 ! ALLOW ALI SUL ION
! fitted to C-S s 9/26/92 (FL)
S HS 275.000 1.3250 ! ALLOW SUL ION
! methanethiol pure solvent, adm jr., 6/22/92
SM CT2 214.000 1.8160 ! ALLOW SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
SM CT3 214.000 1.8160 ! ALLOW SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
SM SM 173.000 2.0290 ! ALLOW SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
SS CS 205.000 1.8360 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
ANGLES
!
!V(angle) = Ktheta(Theta - Theta0)**2
!
!V(Urey-Bradley) = Kub(S - S0)**2
!
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley)
!S0: A
!
!atom types Ktheta Theta0 Kub S0
!
CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO
! JES 8/25/89
CE1 CE1 CT3 48.00 123.50 !
! for 2-butene, yin/adm jr., 12/95
CE1 CT2 CT3 32.00 112.20 !
! for 1-butene; from propene, yin/adm jr., 12/95
CE2 CE1 CT2 48.00 126.00 !
! for 1-butene; from propene, yin/adm jr., 12/95
CE2 CE1 CT3 47.00 125.20 !
! for propene, yin/adm jr., 12/95
CP1 N C 60.000 117.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 C 52.000 112.3000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 CC 52.000 112.3000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 CD 50.000 112.3000 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP2 CP1 70.000 108.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 CP2 CP2 70.000 108.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 N C 60.000 117.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 N CP1 100.000 114.2000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 NP CP1 100.000 111.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CPA CPB C 70.000 126.7400 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CPA CPM CPA 94.200 125.1200 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPA NPH CPA 139.300 103.9000 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB C C 70.000 121.5000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CPB CPB C 70.000 126.7500 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CPB CPB CPA 30.800 106.5100 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPH2 NR1 CPH1 130.000 107.5000 ! ALLOW ARO
! his, adm jr., 6/27/90
CPH2 NR2 CPH1 130.000 104.0000 ! ALLOW ARO
! his, adm jr., 6/27/90
CPH2 NR3 CPH1 145.000 108.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
CPM CPA CPB 61.600 124.0700 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPT CA CA 60.000 118.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CPT CPT CA 60.000 122.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CPT CY CA 120.000 107.40 25.00 2.26100 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CPT NY CA 110.000 108.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CT1 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
CT1 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT1 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO
! PARALLH19 (JES)
CT1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
CT1 CT2 CPH1 58.350 113.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted
CT1 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT1 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
CT2 CA CA 45.800 122.3000 ! ALLOW ALI ARO
! PARALLH19 (JES)
CT2 CPB CPA 65.000 126.7400 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT2 CPB CPB 65.000 126.7500 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT2 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS
CT2 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
CT2 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
CT2 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 CT2 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! from CT2 CT1 C, for lactams, adm jr.
CT2 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
CT2 CT2 CPB 70.000 113.0000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT2 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT2 CT2 CT2 58.350 113.60 11.16 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 CT3 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT2 CY CA 45.800 129.4000 ! ALLOW ARO
!adm jr., 5/08/91, indole CCDB structure search
CT2 CY CPT 45.800 124.0000 ! ALLOW ARO
!adm jr., 5/08/91, indole CCDB structure search
CT2 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO
! 107.5->120.0 to make planar Arg (KK)
CT2 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
CT2 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP
! adm jr. 5/02/91, acetic acid pure solvent
CT3 CA CA 45.800 122.3000 ! ALLOW ALI ARO
! toluene, adm jr., 3/7/92
CT3 CPB CPA 65.000 126.7400 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT3 CPB CPB 65.000 126.7500 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
CT3 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS
CT3 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/09/92, for ALA cter
CT3 CT1 CT1 53.350 108.50 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT1 CT2 53.350 114.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT1 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO
! ethylbenzene, adm jr., 3/7/92
CT3 CT2 CPH1 58.350 113.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted
CT3 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT3 CT2 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT2 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO
! methylguanidinium, adm jr., 3/26/92
CT3 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
CT3 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP
! adm jr. 5/02/91, acetic acid pure solvent
CT3 S CT2 34.000 95.0000 ! ALLOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
CY CPT CA 160.000 130.6000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CY CPT CPT 110.000 107.4000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
CY CT2 CT1 58.350 114.0000 ! ALLOW ARO
! from TRP crystal, JWK
CY CT2 CT3 58.350 114.0000 ! ALLOW ARO
! from TRP crystal, JWK
FE NPH CPA 96.150 128.0500 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
FE NR2 CPH1 30.000 133.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
FE NR2 CPH2 30.000 123.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
H NH1 C 34.000 123.0000 ! ALLOW PEP POL ARO
! NMA Vib Modes (LK)
H NH1 CT1 35.000 117.0000 ! ALLOW PEP POL ARO ALI
! NMA Vibrational Modes (LK)
H NH1 CT2 35.000 117.0000 ! ALLOW PEP POL ARO ALI
! NMA Vibrational Modes (LK)
H NH1 CT3 35.000 117.0000 ! ALLOW PEP POL ARO ALI
! NMA Vibrational Modes (LK)
H NH2 CC 50.000 120.0000 ! ALLOW POL PEP ARO
! his, adm jr. 8/13/90 acetamide geometry and vibrations
H NH2 H 23.000 120.0000 ! ALLOW POL
! adm jr. 8/13/90 acetamide geometry and vibrations
H NR1 CPH1 30.000 125.50 20.00 2.15000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NR1 CPH2 30.000 127.00 20.00 2.14000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NR3 CPH1 25.000 126.00 15.00 2.13000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NR3 CPH2 25.000 126.00 15.00 2.09000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NY CA 28.000 126.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
H NY CPT 28.000 126.0000 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
H OH1 CA 65.000 108.0000 ! ALLOW ALC ARO
! JES 8/25/89 phenol
H OH1 CD 55.000 115.0000 ! ALLOW ALC ARO PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
H OH1 CT1 57.500 106.0000 ! ALLOW ALC ARO ALI
! methanol vib fit EMB 11/21/89
H OH1 CT2 57.500 106.0000 ! ALLOW ALC ARO ALI
! methanol vib fit EMB 11/21/89
H OH1 CT3 57.500 106.0000 ! ALLOW ALC ARO ALI
! methanol vib fit EMB 11/21/89
HA C C 50.000 120.5000 ! ALLOW PEP POL ARO
! Heme vinyl substituent (KK from propene (JCS))
HA C CPB 50.000 120.0000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
HA C HA 50.000 118.0000 ! ALLOW PEP POL ARO
! Heme vinyl substituent (KK from propene (JCS))
HA CA CA 29.000 120.00 25.00 2.15250 ! ALLOW ARO
! trp, adm jr., 10/02/89
HA CA CPT 41.000 122.0000 ! ALLOW ARO
!adm jr., 5/08/91, indole CCDB structure search
HA CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HA CP2 CP1 33.430 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP2 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP2 CP3 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CPM CPA 12.700 117.4400 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
HA CPM FE 0.000 180.0000 ! ALLOW HEM
! Heme (6-liganded): for "ic para" only (KK 05/13/91)
HA CS CT3 34.600 110.10 22.53 2.17900 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CS HA 35.500 108.40 14.00 1.77500 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CT1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA CT1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA CT1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT1 HA 35.500 109.00 5.40 1.80200 ! TEST for test cpd
! based on HA CT2 HA
HA CT2 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA CT2 CA 49.300 107.5000 ! ALLOW ALI ARO
! PARALLH19 (JES)
HA CT2 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HA CT2 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA CT2 CE1 45.00 111.50 !
! for 1-butene; from propene, yin/adm jr., 12/95
HA CT2 CPB 50.000 109.5000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
HA CT2 CPH1 33.430 109.5000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
HA CT2 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
HA CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT2 CY 33.430 109.5000 ! ALLOW ARO
! ADM JR., 10/02/89, from CT2CT2HA (U-B OMITTED), FOR JOANNA
HA CT2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT3 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA CT3 CA 49.300 107.5000 ! ALLOW ALI ARO
! toluene, adm jr. 3/7/92
HA CT3 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HA CT3 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA CT3 CE1 42.00 111.50 !
! for 2-butene, yin/adm jr., 12/95
HA CT3 CPB 50.000 109.5000 ! ALLOW HEM
! Heme (6-liganded): substituents (KK 05/13/91)
HA CT3 CPH1 33.430 109.5000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
HA CT3 CS 34.600 110.10 22.53 2.17900 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
HA CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CY CA 20.000 126.40 25.00 2.18600 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HA CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HA1 CE1 CE1 52.00 119.50 !
! for 2-butene, yin/adm jr., 12/95
HA1 CE1 CE2 42.00 118.00 !
! for propene, yin/adm jr., 12/95
HA1 CE1 CT2 40.00 116.00 !
! for 1-butene; from propene, yin/adm jr., 12/95
HA1 CE1 CT3 22.00 117.00 !
! for propene, yin/adm jr., 12/95
HA2 CE2 CE1 45.00 120.50 !
! for propene, yin/adm jr., 12/95
HA2 CE2 CE2 55.50 120.50 !
! for ethene, yin/adm jr., 12/95
HA2 CE2 HA2 19.00 119.00 !
! for propene, yin/adm jr., 12/95
HB CP1 C 50.000 112.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CP1 CC 50.000 112.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CP1 CD 50.000 112.0000 ! ALLOW PEP POL PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CP1 CP2 35.000 118.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB CT1 C 50.000 109.5000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT1 CC 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HB CT1 CD 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
HB CT1 CT1 35.000 111.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT1 CT2 35.000 111.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT1 CT3 35.000 111.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT2 C 50.000 109.5000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT2 CC 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HB CT2 CD 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
HB CT2 HB 36.000 115.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB CT3 C 50.000 109.5000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HC NC2 C 49.000 120.0000 ! ALLOW POL PEP ARO
! 35.3->49.0 GUANIDINIUM (KK)
HC NC2 CT2 40.400 120.0000 ! ALLOW POL ALI
! 107.5->120.0 to make planar Arg (KK)
HC NC2 CT3 40.400 120.0000 ! ALLOW POL ALI
! methylguanidinium, adm jr., 3/26/92
HC NC2 HC 25.000 120.0000 ! ALLOW POL
! 40.0->25.0 GUANIDINIUM (KK)
HC NH2 CT2 50.000 111.0000 ! ALLOW POL
! from HC NH2 CT3, neutral glycine, adm jr.
HC NH2 CT3 50.000 111.0000 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
HC NH2 HC 39.000 106.5000 ! ALLOW POL
! 40.0->25.0 GUANIDINIUM (KK)
HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
! new stretch and bend; methylammonium (KK 03/10/92)
HC NH3 CT2 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
! new stretch and bend; methylammonium (KK 03/10/92)
HC NH3 CT3 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
! new stretch and bend; methylammonium (KK 03/10/92)
HC NH3 HC 44.000 109.5000 ! ALLOW POL
! new stretch and bend; methylammonium (KK 03/10/92)
HC NP CP1 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HC NP CP3 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HC NP HC 51.000 107.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HP CA CA 30.000 120.00 22.00 2.15250 ! ALLOW ARO
! JES 8/25/89 benzene
HP CA CPT 30.000 122.00 22.00 2.14600 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
HP CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HP CY CA 32.000 126.40 25.00 2.18600 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
HP CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO
! JWK 05/14/91 new theta0 and r0UB from indole
HR1 CPH1 CPH1 22.000 130.00 15.00 2.21500 ! ALLOW ARO
! adm jr., 6/27/90, his
HR3 CPH1 CPH1 25.000 130.00 20.00 2.20000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HS S CT2 38.800 95.0000 ! ALLOW SUL ION ALI
! methanethiol pure solvent, adm jr., 6/22/92
HS S CT3 43.000 95.0000 ! ALLOW SUL ION ALI
! methanethiol pure solvent, adm jr., 6/22/92
HT OT HT 55.000 104.5200 ! ALLOW WAT
! TIP3P GEOMETRY, ADM JR.
N C CP1 20.000 112.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT1 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT2 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT3 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 C 50.000 108.2000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 CC 50.000 108.2000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 CD 50.000 108.2000 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 CP2 70.000 110.8000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 HB 48.000 112.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP3 CP2 70.000 110.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP3 HA 48.000 108.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC2 C NC2 52.000 120.00 90.00 2.36420 ! ALLOW POL PEP ARO
! changed from 60.0/120.3 for guanidinium (KK)
NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL
! arg, (DS)
NC2 CT2 HA 51.500 107.5000 ! ALLOW ALI POL
! arg, (DS)
NC2 CT3 HA 51.500 107.5000 ! ALLOW ALI POL
! methylguanidinium, adm jr., 3/26/92
NH1 C CP1 80.000 116.5000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH1 C CT1 80.000 116.5000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
NH1 C CT2 80.000 116.5000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
NH1 C CT3 80.000 116.5000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
NH1 CT1 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
NH1 CT1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 5/02/91, acetic acid pure solvent
NH1 CT1 CT1 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 HB 48.000 108.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT2 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT2 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 5/20/92, for asn,asp,gln,glu and cters
NH1 CT2 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 5/02/91, acetic acid pure solvent
NH1 CT2 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! from NH1 CT1 CT2, for lactams, adm jr.
NH1 CT2 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO
! from NH1 CT3 HA, for lactams, adm jr.
NH1 CT2 HB 48.000 108.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT3 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO
! NMA crystal (JCS)
NH2 CC CP1 80.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH2 CC CT1 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 CC CT3 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 CC HA 44.000 111.00 50.00 1.98000 ! ALLOW POL
! adm jr., 5/13/91, formamide geometry and vibrations
NH2 CT2 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
! 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
! adm jr. 4/10/91, acetamide update
OB CD CP1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
OB CD CT1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
OB CD CT2 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
OB CD CT3 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
OC CA CA 40.000 120.0000 ! ALLOW POL ARO
! adm jr. 8/27/91, phenoxide
OC CC CP1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION
! adm jr. 7/23/91, correction, ACETATE (KK)
OC CC CT2 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION
! adm jr. 7/23/91, correction, ACETATE (KK)
OC CC CT3 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION
! adm jr. 7/23/91, correction, ACETATE (KK)
OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO
! adm jr. 7/23/91, correction, ACETATE (KK)
OC CT2 CT3 65.000 122.0000 ! ALLOW ALC
! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
OC CT2 HA 65.000 118.3000 ! ALLOW ALC
! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
OC CT3 HA 65.000 118.3000 ! ALLOW ALC
! methoxide 6-31+G* geom/freq, adm jr., 6/1/92
OH1 CA CA 45.200 120.0000 ! ALLOW ARO ALC
! PARALLH19 WITH [122.3] (JES)
OH1 CD CT2 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC
! adm jr, 10/17/90, acetic acid vibrations
OH1 CD CT3 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC
! adm jr, 10/17/90, acetic acid vibrations
OH1 CD OB 50.000 123.00 210.00 2.26200 ! ALLOW PEP POL ARO ALC
! adm jr, 10/17/90, acetic acid vibrations
OH1 CT1 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT1 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT1 HA 45.900 108.8900 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT2 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT2 CT2 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT2 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT2 HA 45.900 108.8900 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT3 HA 45.900 108.8900 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OM CM FE 35.000 180.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
OM FE NPH 5.000 90.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
OM OM FE 0.000 180.0000 ! ALLOW HEM
! Heme (6-liganded): ligand links (KK 05/13/91)
OS CD CP1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
OS CD CT1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP
! adm jr., 4/05/91, for PRES CT1 from methylacetate
OS CD CT2 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP
! adm jr., 4/05/91, for PRES CT1 from methylacetate
OS CD CT3 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP
! adm jr., 4/05/91, for PRES CT1 from methylacetate
OS CD OB 90.000 125.90 160.00 2.25760 ! ALLOW PEP POL
! adm jr. 3/19/92, from lipid methyl acetate
OS CT2 HA 60.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for PRES CT1 from methyl acetate
OS CT3 HA 60.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for PRES CT1 from methyl acetate
S CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION
! as in expt.MeEtS & DALC crystal, 5/15/92
S CT2 CT2 58.000 114.5000 ! ALLOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
S CT2 CT3 58.000 114.5000 ! ALLOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
S CT2 HA 46.100 111.3000 ! ALLOW ALI SUL ION
! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90
S CT3 HA 46.100 111.3000 ! ALLOW ALI SUL ION
! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90
SM CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION
! as in expt.MeEtS & DALC crystal, 5/15/92
SM CT2 HA 38.000 111.0000 ! ALLOW ALI SUL ION
! new S-S atom type 8/24/90
SM CT3 HA 38.000 111.0000 ! ALLOW ALI SUL ION
! new S-S atom type 8/24/90
SM SM CT2 72.500 103.3000 ! ALLOW ALI SUL ION
! expt. dimethyldisulfide, 3/26/92 (FL)
SM SM CT3 72.500 103.3000 ! ALLOW ALI SUL ION
! expt. dimethyldisulfide, 3/26/92 (FL)
SS CS CT3 55.000 118.0000 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
SS CS HA 40.000 112.3000 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types Kchi n delta
!
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 HA2 5.2000 2 180.00 !
! for propene, yin/adm jr., 12/95
CT3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO
! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2
CT3 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP
! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
CT3 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI
! ethylbenzene ethyl rotation, adm jr. 3/7/92
CT3 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO
! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CT3 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO
! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CT3 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CT3 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI
! alkane update, adm jr., 3/2/92, butane trans/gauche
CT3 CT2 CT2 CT3 0.1500 1 0.00 ! ALLOW ALI
! alkane update, adm jr., 3/2/92, butane trans/gauche
CT3 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO
! from ethylbenzene, adm jr., 3/7/92
CT3 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO
! from ethylbenzene, adm jr., 3/7/92
CT3 CT2 S CT3 0.2400 1 180.00 ! ALOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
CT3 CT2 S CT3 0.3700 3 0.00 ! ALOW ALI SUL ION
! DTN 8/24/90
CT3 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT3 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT3 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP
! Revised to adjust NMA cis/trans energy difference. (LK)
CT3 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
CT3 S CT2 CT2 0.2400 1 180.00 ! ALOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
CT3 S CT2 CT2 0.3700 3 0.00 ! ALOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
CT3 SM SM CT3 1.0000 1 0.00 ! ALLOW ALI SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
CT3 SM SM CT3 4.1000 2 0.00 ! ALLOW ALI SUL ION
! mp 6-311G** dimethyldisulfide, 3/26/92 (FL)
CT3 SM SM CT3 0.9000 3 0.00 ! ALLOW ALI SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
CY CA NY CPT 5.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
CY CPT CA CA 3.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
CY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
H NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
H NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
H NH1 C CT2 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
H NH1 C CT3 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
H NH1 CT1 C 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
H NH1 CT1 CC 0.0000 1 0.00 ! ALLOW PEP POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
H NH1 CT1 CD 0.0000 1 0.00 ! ALLOW PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
H NH1 CT1 CT1 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
H NH1 CT1 CT2 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
H NH1 CT1 CT3 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
H NH1 CT2 C 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
H NH1 CT2 CC 0.0000 1 0.00 ! ALLOW PEP POL
! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
H NH1 CT2 CD 0.0000 1 0.00 ! ALLOW PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
H NH1 CT2 CT2 0.0000 1 0.00 ! ALLOW PEP
! from H NH1 CT2 CT3, for lactams, adm jr.
H NH1 CT2 CT3 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
H NH2 CC CT1 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
! adm jr. 4/10/91, acetamide update
H NH2 CC CT2 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
! adm jr. 4/10/91, acetamide update
H NH2 CC CT3 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
! adm jr. 4/10/91, acetamide update
H NH2 CC CP1 2.5000 2 180.00 ! ALLOW PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
H NR1 CPH1 CPH1 1.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 7/20/89
H NR1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H
H NR1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H
H NR3 CPH1 CPH1 1.4000 2 180.00 ! ALLOW ARO
! his, adm jr., 6/27/90
H NR3 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA
H NR3 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO
! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA
H NY CA CY 0.8000 2 180.00 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
H NY CPT CA 0.8000 2 180.00 ! ALLOW ARO
!adm jr., 12/30/91, for jwk
H NY CPT CPT 0.8000 2 180.00 ! ALLOW ARO
! JWK 05/14/91 fit to indole
H OH1 CA CA 0.9900 2 180.00 ! ALLOW ARO ALC
! phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92
H OH1 CT1 CT1 1.3300 1 0.00 ! ALLOW ALC
! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT1 CT1 0.1800 2 0.00 ! ALLOW ALC
! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT1 CT1 0.3200 3 0.00 ! ALLOW ALC
! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT1 CT3 1.3300 1 0.00 ! ALLOW ALC
! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT1 CT3 0.1800 2 0.00 ! ALLOW ALC
! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT1 CT3 0.3200 3 0.00 ! ALLOW ALC
! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT1 1.3000 1 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT1 0.3000 2 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT1 0.4200 3 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT2 1.3000 1 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT2 0.3000 2 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT2 0.4200 3 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT3 1.3000 1 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT3 0.3000 2 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
H OH1 CT2 CT3 0.4200 3 0.00 ! ALLOW ALC
! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
HA CA CA CA 3.5000 2 180.00 ! ALLOW ARO
! adm jr., 10/02/89
HA CA CA CPT 3.5000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CA CA HA 2.5000 2 180.00 ! ALLOW ARO
! ADM JR., 10/02/89
HA CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO
! TRP (JES)
HA CA CPT CY 4.0000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CA CY CPT 1.2000 2 180.00 ! ALLOW ARO
! JWK
HA CA CY CT2 1.2000 2 180.00 ! ALLOW ARO
! JWK
HA CA NY CPT 3.0000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CA NY H 1.0000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL
! adm jr. 4/10/91, acetamide update
HA CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
HA CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89
HA CT2 CY CA 0.2500 2 180.00 ! ALLOW ARO
! JWK
HA CT2 CY CPT 0.2500 2 180.00 ! ALLOW ARO
! JWK
HA CT2 NH1 C 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
HA CT2 NH1 H 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
HA CT2 S CT3 0.2800 3 0.00 ! ALLOW ALI SUL ION
! DTN 8/24/90
HA CT3 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89
HA CT3 CS HA 0.1600 3 0.00 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA CT3 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
HA CT3 NH1 C 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
HA CT3 NH1 H 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
HA CT3 S CT2 0.2800 3 0.00 ! ALLOW ALI SUL ION
! DTN 8/24/90
HA CY CA CPT 1.2000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CY CA HA 1.2000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO
! JWK 09/05/89
HA1 CE1 CE2 HA2 5.2000 2 180.00 !
! for propene, yin/adm jr., 12/95
HA1 CE1 CT2 HA 0.8700 3 0.00 !
! for butene, yin/adm jr., 12/95
HA1 CE1 CT2 CT3 0.1200 3 0.00 !
! for butene, yin/adm jr., 12/95
HA1 CE1 CT3 HA 0.3400 3 0.00 !
! for butene, yin/adm jr., 12/95
HA2 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)
IMPROPER
!
!V(improper) = Kpsi(psi - psi0)**2
!
!Kpsi: kcal/mole/rad**2
!psi0: degrees
!note that the second column of numbers (0) is ignored
!
!atom types Kpsi psi0
!
CPB CPA NPH CPA 20.8000 0 0.0000 ! ALLOW HEM
! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
CPB X X 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))
HA2 HA2 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)
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
!
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
HA1 0.000000 -0.031000 1.250000 !
! for propene, yin/adm jr., 12/95
HA2 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
!HA1 0.000000 -0.031000 1.250000
!HA2 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
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
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