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Commit c7aa1d00 authored by kyleabeauchamp's avatar kyleabeauchamp
Browse files

Merge remote-tracking branch 'upstream/master' into vagrant

parents aea4e454 f7127d33
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Showing with 18713 additions and 61 deletions
wrappers/python/simtk/openmm/app/internal/charmm/_charmmfile.py
View file @ c7aa1d00
......@@ -47,7 +47,6 @@ class CharmmFile(object):
"""
def __init__(self, fname, mode='r'):
self.closed = False
if mode not in ('r', 'w'):
raise ValueError('Cannot open CharmmFile with mode "%s"' % mode)
if mode == 'r':
......@@ -58,6 +57,7 @@ class CharmmFile(object):
self._handle = open(fname, mode)
except IOError, e:
raise CharmmFileError(str(e))
self.closed = False
self.line_number = 0
def write(self, *args, **kwargs):
......
wrappers/python/simtk/openmm/app/internal/charmm/topologyobjects.py
View file @ c7aa1d00
......@@ -42,6 +42,32 @@ TINY = 1e-8
# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
def _tracking(fcn):
""" Decorator to indicate the list has changed """
def new_fcn(self, *args):
self.changed = True
return fcn(self, *args)
return new_fcn
class TrackedList(list):
"""
This creates a list type that allows you to see if anything has changed
"""
def __init__(self, arg=[]):
self.changed = False
list.__init__(self, arg)
__delitem__ = _tracking(list.__delitem__)
append = _tracking(list.append)
extend = _tracking(list.extend)
__setitem__ = _tracking(list.__setitem__)
# Python 3 does not have __delslice__, but make sure we override it for Python 2
if hasattr(TrackedList, '__delslice__'):
TrackedList.__delslice__ = _tracking(TrackedList.__delslice__)
# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
class AtomType(object):
"""
Atom types can either be compared by indexes or names. Can be assigned with
......@@ -61,6 +87,9 @@ class AtomType(object):
- _member_number (int, private) : The order in which this atom type
was 'added' this is used to make sure that atom types added
last have priority in assignment in the generated hash tables
- nbfix (dict) : Dictionary that maps nbfix terms with other atom types.
Dict entries are (rmin, epsilon) -- precombined values
for that particular atom pair
Example:
>>> at = AtomType('HA', 1, 1.008, 1)
>>> at.name, at.number
......@@ -93,6 +122,9 @@ class AtomType(object):
self.atomic_number = atomic_number
# We have no LJ parameters as of yet
self.epsilon = self.rmin = self.epsilon_14 = self.rmin_14 = None
# Store each NBFIX term as a dict with the atom type string matching to
# a 2-element tuple that is rmin, epsilon
self.nbfix = dict()
def __eq__(self, other):
"""
......@@ -123,6 +155,12 @@ class AtomType(object):
""" The integer representation of an AtomType is its index """
return self.number
def add_nbfix(self, typename, rmin, epsilon, rmin14, epsilon14):
""" Adds a new NBFIX exclusion for this atom """
if rmin14 is None: rmin14 = rmin
if epsilon14 is None: epsilon14 = epsilon
self.nbfix[typename] = (rmin, epsilon, rmin14, epsilon14)
def __str__(self):
return self.name
......@@ -311,7 +349,7 @@ class Atom(object):
# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
class AtomList(list):
class AtomList(TrackedList):
""" A list of Atom instances. """
def unmark(self):
......@@ -424,7 +462,7 @@ class ResidueList(list):
elif (self._last_residue != (resname, resnum) or
system != self._last_residue.system):
if (self._last_residue.idx == resnum and
system == self._last_residue.system):
self._last_residue.system == system):
lresname = self._last_residue.resname
warnings.warn('Residue %d split into separate residues %s '
'and %s' % (resnum, lresname, resname),
......@@ -1047,28 +1085,6 @@ class _CmapGrid(object):
# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
def _tracking(fcn):
""" Decorator to indicate the list has changed """
def new_fcn(self, *args):
self.changed = True
return fcn(self, *args)
return new_fcn
class TrackedList(list):
"""
This creates a list type that allows you to see if anything has changed
"""
def __init__(self, arg=[]):
self.changed = False
list.__init__(self, arg)
__delitem__ = _tracking(list.__delitem__)
append = _tracking(list.append)
extend = _tracking(list.extend)
__setitem__ = _tracking(list.__setitem__)
# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
if __name__ == '__main__':
import doctest
doctest.testmod()
wrappers/python/simtk/unit/doctests.py
View file @ c7aa1d00
......@@ -41,12 +41,12 @@ Quantity(value=1.0, unit=calorie)
>>> print(joule.conversion_factor_to(calorie))
0.239005736138
>>> c.in_units_of(joules)
Quantity(value=4.1840000000000002, unit=joule)
Quantity(value=4.184, unit=joule)
>>> j = 1.0*joules
>>> j
Quantity(value=1.0, unit=joule)
>>> j.in_units_of(calories)
Quantity(value=0.23900573613766729, unit=calorie)
Quantity(value=0.2390057361376673, unit=calorie)
>>> j/joules
1.0
>>> print(j/calories)
......@@ -58,7 +58,7 @@ Quantity(value=0.23900573613766729, unit=calorie)
>>> c**2
Quantity(value=1.0, unit=calorie**2)
>>> (c**2).in_units_of(joule*joule)
Quantity(value=17.505856000000001, unit=joule**2)
Quantity(value=17.505856, unit=joule**2)
>>> ScaledUnit(1000.0, kelvin, "kilokelvin", "kK")
ScaledUnit(factor=1000.0, master=kelvin, name='kilokelvin', symbol='kK')
......@@ -252,12 +252,12 @@ Collections of numbers can also be used as values.
>>> print(s4)
((1, 2, 3), (4, 5, 6)) cm
>>> print(s4 / millimeters)
[(10.0, 20.0, 30.0), (40.0, 50.0, 60.0)]
((10.0, 20.0, 30.0), (40.0, 50.0, 60.0))
>>> t = (1,2,3) * centimeters
>>> print(t)
(1, 2, 3) cm
>>> print(t / millimeters)
[10.0, 20.0, 30.0]
(10.0, 20.0, 30.0)
Numpy examples are commented out because not all systems have numpy installed
# >>> import numpy
......@@ -772,7 +772,7 @@ Examples
Creating a new ScaledUnit:
>>> mC = milli * ScaledUnit(4.184, joule, "calorie", "cal")
>>> mC
ScaledUnit(factor=0.0041840000000000002, master=joule, name='millicalorie', symbol='mcal')
ScaledUnit(factor=0.004184, master=joule, name='millicalorie', symbol='mcal')
Creating a new Unit:
>>> ms = milli * second
......@@ -795,7 +795,7 @@ Examples
Formatting of Quantities
>>> x = 5.439999999 * picosecond
>>> x
Quantity(value=5.4399999990000003, unit=picosecond)
Quantity(value=5.439999999, unit=picosecond)
>>> x.format("%.3f")
'5.440 ps'
......
wrappers/python/simtk/unit/quantity.py
View file @ c7aa1d00
......@@ -545,10 +545,7 @@ class Quantity(object):
pass
if factor_is_identity:
# No multiplication required
if (self.unit is new_unit):
result = self
else:
result = Quantity(self._value, new_unit)
result = Quantity(copy.deepcopy(self._value), new_unit)
else:
try:
# multiply operator, if it exists, is preferred
......@@ -558,18 +555,7 @@ class Quantity(object):
value = factor * self._value # works for number, numpy.array, or vec3, e.g.
result = Quantity(value, new_unit)
except TypeError:
# list * float fails with TypeError
# Presumably a list type
# deep copy
value = self._value[:] # deep copy
# convert tuple to list
try:
value[0] = value[0] # tuple is immutable
except TypeError:
# convert immutable tuple to list
value = []
for i in self._value:
value.append(i)
value = copy.deepcopy(self._value)
result = Quantity(self._scale_sequence(value, factor, post_multiply), new_unit)
if (new_unit.is_dimensionless()):
return result._value
......@@ -579,20 +565,29 @@ class Quantity(object):
def _scale_sequence(self, value, factor, post_multiply):
try:
if post_multiply:
if isinstance(self._value, tuple):
value = tuple([x*factor for x in value])
else:
for i in range(len(value)):
value[i] = value[i]*factor
value = value*factor
else:
if isinstance(self._value, tuple):
value = tuple([factor*x for x in value])
value = factor*value
except TypeError:
try:
if post_multiply:
if isinstance(value, tuple):
value = tuple([x*factor for x in value])
else:
for i in range(len(value)):
value[i] = value[i]*factor
else:
if isinstance(value, tuple):
value = tuple([factor*x for x in value])
else:
for i in range(len(value)):
value[i] = factor*value[i]
except TypeError as ex:
if isinstance(value, tuple):
value = tuple([self._scale_sequence(x, factor, post_multiply) for x in value])
else:
for i in range(len(value)):
value[i] = factor*value[i]
except TypeError as ex:
for i in range(len(value)):
value[i] = self._scale_sequence(value[i], factor, post_multiply)
value[i] = self._scale_sequence(value[i], factor, post_multiply)
return value
......
wrappers/python/tests/TestAmberPrmtopFile.py
View file @ c7aa1d00
......@@ -8,7 +8,9 @@ import simtk.openmm.app.element as elem
prmtop1 = AmberPrmtopFile('systems/alanine-dipeptide-explicit.prmtop')
prmtop2 = AmberPrmtopFile('systems/alanine-dipeptide-implicit.prmtop')
prmtop3 = AmberPrmtopFile('systems/ff14ipq.parm7')
prmtop4 = AmberPrmtopFile('systems/Mg_water.prmtop')
inpcrd3 = AmberInpcrdFile('systems/ff14ipq.rst7')
inpcrd4 = AmberInpcrdFile('systems/Mg_water.inpcrd')
class TestAmberPrmtopFile(unittest.TestCase):
......@@ -145,8 +147,8 @@ class TestAmberPrmtopFile(unittest.TestCase):
totalMass2 = sum([system2.getParticleMass(i) for i in range(system2.getNumParticles())]).value_in_unit(amu)
self.assertAlmostEqual(totalMass1, totalMass2)
def test_NBFIX(self):
"""Test that prmtop files with modified off-diagonal LJ elements are treated properly"""
def test_NBFIX_LongRange(self):
"""Test prmtop files with NBFIX LJ modifications w/ long-range correction"""
system = prmtop3.createSystem(nonbondedMethod=PME,
nonbondedCutoff=8*angstroms)
# Check the forces
......@@ -173,7 +175,71 @@ class TestAmberPrmtopFile(unittest.TestCase):
ene = ene.value_in_unit(kilocalories_per_mole)
# Make sure the energy is relatively close to the value we get with
# Amber using this force field.
self.assertAlmostEqual(-7099.44989739/ene, 1, places=3)
def test_NBFIX_noLongRange(self):
"""Test prmtop files with NBFIX LJ modifications w/out long-range correction"""
system = prmtop3.createSystem(nonbondedMethod=PME,
nonbondedCutoff=8*angstroms)
# Check the forces
has_nonbond_force = has_custom_nonbond_force = False
nonbond_exceptions = custom_nonbond_exclusions = 0
for force in system.getForces():
if isinstance(force, NonbondedForce):
has_nonbond_force = True
nonbond_exceptions = force.getNumExceptions()
elif isinstance(force, CustomNonbondedForce):
has_custom_nonbond_force = True
custom_nonbond_exceptions = force.getNumExclusions()
force.setUseLongRangeCorrection(False)
self.assertTrue(has_nonbond_force)
self.assertTrue(has_custom_nonbond_force)
self.assertEqual(nonbond_exceptions, custom_nonbond_exceptions)
integrator = VerletIntegrator(1.0*femtoseconds)
# Use reference platform, since it should always be present and
# 'working', and the system is plenty small so this won't be too slow
sim = Simulation(prmtop3.topology, system, integrator, Platform.getPlatformByName('Reference'))
# Check that the energy is about what we expect it to be
sim.context.setPeriodicBoxVectors(*inpcrd3.getBoxVectors())
sim.context.setPositions(inpcrd3.getPositions())
ene = sim.context.getState(getEnergy=True, enforcePeriodicBox=True).getPotentialEnergy()
ene = ene.value_in_unit(kilocalories_per_mole)
# Make sure the energy is relatively close to the value we get with
# Amber using this force field.
self.assertAlmostEqual(-7042.3903307/ene, 1, places=3)
def test_LJ1264(self):
"""Test prmtop with 12-6-4 vdW potential implemented"""
system = prmtop4.createSystem(nonbondedMethod=PME,
nonbondedCutoff=8*angstroms)
# Check the forces
has_nonbond_force = has_custom_nonbond_force = False
nonbond_exceptions = custom_nonbond_exclusions = 0
for force in system.getForces():
if isinstance(force, NonbondedForce):
has_nonbond_force = True
nonbond_exceptions = force.getNumExceptions()
force.setUseDispersionCorrection(False)
elif isinstance(force, CustomNonbondedForce):
self.assertTrue(force.getUseLongRangeCorrection())
has_custom_nonbond_force = True
custom_nonbond_exceptions = force.getNumExclusions()
force.setUseLongRangeCorrection(False)
self.assertTrue(has_nonbond_force)
self.assertTrue(has_custom_nonbond_force)
self.assertEqual(nonbond_exceptions, custom_nonbond_exceptions)
integrator = VerletIntegrator(1.0*femtoseconds)
# Use reference platform, since it should always be present and
# 'working', and the system is plenty small so this won't be too slow
sim = Simulation(prmtop4.topology, system, integrator, Platform.getPlatformByName('Reference'))
# Check that the energy is about what we expect it to be
sim.context.setPeriodicBoxVectors(*inpcrd4.boxVectors)
sim.context.setPositions(inpcrd4.positions)
ene = sim.context.getState(getEnergy=True, enforcePeriodicBox=True).getPotentialEnergy()
ene = ene.value_in_unit(kilocalories_per_mole)
# Make sure the energy is relatively close to the value we get with
# Amber using this force field.
self.assertAlmostEqual(-7307.2735621/ene, 1, places=3)
if __name__ == '__main__':
unittest.main()
wrappers/python/tests/TestCharmmFiles.py
View file @ c7aa1d00
......@@ -100,6 +100,33 @@ class TestCharmmFiles(unittest.TestCase):
totalMass2 = sum([system2.getParticleMass(i) for i in range(system2.getNumParticles())]).value_in_unit(amu)
self.assertAlmostEqual(totalMass1, totalMass2)
def test_NBFIX(self):
"""Tests CHARMM systems with NBFIX Lennard-Jones modifications"""
import warnings
warnings.filterwarnings('ignore', category=CharmmPSFWarning)
psf = CharmmPsfFile('systems/ala3_solv.psf')
crd = CharmmCrdFile('systems/ala3_solv.crd')
params = CharmmParameterSet('systems/par_all36_prot.prm',
'systems/toppar_water_ions.str')
# Box dimensions (found from bounding box)
psf.setBox(32.7119500*angstroms, 32.9959600*angstroms, 33.0071500*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 = psf.createSystem(params, nonbondedMethod=PME,
nonbondedCutoff=8*angstroms)
con = Context(system, VerletIntegrator(2*femtoseconds), plat)
con.setPositions(crd.positions)
state = con.getState(getEnergy=True, enforcePeriodicBox=True)
ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene, 15490.0033559, delta=0.05)
if __name__ == '__main__':
unittest.main()
wrappers/python/tests/systems/Mg_water.inpcrd 0 → 100644
View file @ c7aa1d00
default_name
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13.5841175 16.0443975 -0.0385710 13.2440138 15.3834752 0.5645401
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0.7072678 0.1353740 0.5522137 0.0106390 0.0008363 0.3231599
-0.1529070 0.2192901 0.8105173 0.5255013 -0.3589025 0.5037010
0.0742731 0.1247117 0.1714649 -0.2175685 0.2981275 0.0862165
0.0573403 -0.1207914 -0.0505529 -0.1711239 0.1244868 -0.3265644
0.5591703 0.6859464 0.3133545 -0.7904675 0.2066753 0.4800569
0.0322813 0.1204564 0.2789256 -0.0642229 0.3320497 0.0491761
-0.2001121 1.0242207 0.3572648 -0.4531824 -0.0241984 -0.1906331
0.1522270 -0.4123607 -0.3932875 0.5920680 0.4021117 -1.1468423
0.0656864 -0.1352740 0.1121382 -0.2791575 0.3241058 -1.1620702
-0.0380177 -0.3562877 -0.4071825 0.1918860 0.1608563 -0.5839496
1.0953857 0.3016062 -1.5374186 -0.4527185 0.0820400 -0.0110079
-0.0757150 0.1939599 -0.0464195 -0.1468366 -0.0931605 -0.5368355
-0.1411447 0.0605170 0.0553854 0.3395627 0.2227286 0.0849709
0.0906974 0.2931363 0.0808480 1.1714332 -0.1390957 -0.1395441
0.0988064 -0.1404966 0.0632396 0.1673706 0.0676351 -0.8138404
-0.7410278 -0.2810206 0.1307523 0.1297197 -0.0957902 -0.1819355
0.2430213 0.5689821 0.7019204 -0.1548270 0.5974304 -0.9996357
-0.0409148 0.0282700 -0.0049092 0.3874333 1.1283459 -0.3909228
-0.3396483 -0.2801643 -0.3677024 -0.0248915 0.0161006 0.1177580
-0.2709406 0.4075829 0.3577215 0.3582185 0.3993374 0.3127149
-0.3326720 0.2539725 -0.1454544 -1.1705843 -0.7210703 -0.9494431
-0.1044212 0.6615529 0.3394818 -0.2157475 -0.3139513 -0.0745825
-0.0797204 0.1256949 0.1837078 -0.3415086 -0.3791736 -0.1191132
-0.1051713 0.0428667 0.2572551 -0.1184718 0.1727362 0.1766945
-0.0731983 -0.0737025 0.0096320 0.0463899 -0.1307133 -0.1169712
0.9376239 -0.3956075 0.1008981 -0.2953373 -0.2953202 0.2007895
0.2258659 -0.0099218 -0.0056263 0.3918711 -1.1715976 -0.2119886
-0.0783705 0.6393514 0.2332187 -0.0781508 -0.3087151 0.1564197
-0.2166742 -0.1066533 -0.5587978 0.1474697 -1.0368325 -0.3104187
-0.0401297 -0.0214261 0.0511961 0.4925624 0.4858883 -1.9637184
0.5099194 -1.6174134 -0.0789637 0.1747782 -0.2943968 0.2289728
0.1816753 -0.4786751 0.9296713 0.0233411 -0.4927005 0.4886941
0.0474036 -0.2546340 -0.0539601 0.1737896 -0.3192477 0.0388878
-0.2897393 -0.4304711 0.6879457 0.0939125 -0.1326088 -0.0938290
0.5915252 0.0851712 0.2763665 0.5725006 0.0155833 0.1556373
0.1049749 0.1034707 -0.2057427 0.0229734 0.5926557 0.6994493
-0.1292689 0.6533735 0.6591679 -0.0831475 -0.2094682 -0.1414605
0.8953989 -1.3044444 0.3276372 0.6067215 1.0563864 0.3761630
-0.1178608 0.0338288 0.1761758 -0.1093441 0.2209270 -0.3941016
0.1100970 0.4142570 0.2455593 0.0099003 -0.1924303 -0.1259278
-0.5039542 0.7429083 -0.7526362 -0.1540479 -0.9474668 0.9817209
-0.0570336 0.2782334 -0.3544690 0.2823929 0.4470828 0.0720086
-0.5918243 0.1785766 -0.5417430 0.0389808 -0.1299517 -0.1772103
-0.9682134 -0.3418418 -0.7319377 -0.2510048 -0.5165638 0.3931600
-0.0145689 -0.1923169 0.1567077 0.2363853 -0.4227549 -0.4247164
-0.5709604 0.7833681 0.3461771 0.0256614 -0.3655953 -0.1152402
0.2995451 -0.4207252 -0.3266064 -0.5742509 0.4624784 -0.3134577
-0.1821045 -0.0640018 -0.2501222 0.8333917 -0.6942590 -0.1350713
-0.7311947 0.5103956 -0.5804864 0.2121480 -0.1833040 -0.2412843
0.6700659 -0.7872621 0.4631774 -0.3063560 -0.4911666 -0.3184633
-0.2054434 -0.0302497 -0.0732976 -0.2823263 0.0546432 -0.4473244
-0.1596632 -0.4524174 -0.0406171 -0.0675635 -0.1768585 0.4559224
0.0292204 0.4068306 -0.8080317 0.3880992 0.0224312 0.6718270
-0.0922740 0.0792745 0.1855451 0.6174663 0.1675329 -0.3291392
-0.0755275 0.6782544 0.2206075 0.0757345 -0.2729096 0.1019375
-0.3869481 0.4351847 0.4873434 0.0145544 -0.2050505 0.6301493
0.2285055 -0.1222371 0.0814240 1.1574758 0.0857758 0.2444381
1.0400766 0.5738419 0.4738514 -0.2227974 -0.2350993 0.2005291
-0.6201370 -0.0561018 -0.0182836 -0.3635021 -0.4692507 -0.3903500
0.3274176 -0.0082131 -0.3054943 0.4626335 0.0729578 -0.1949739
0.6757825 0.4148079 -0.2689513 0.1662249 -0.2502310 0.0704008
-0.2327083 -0.7333074 -0.2429962 -0.0874280 -0.8954311 -0.1929260
0.1712215 0.0230629 -0.0319800 0.1209710 0.3009482 0.0726330
-0.9181626 -0.3228051 -0.3110424 -0.0296518 0.3683303 -0.3078614
-0.1645680 0.9324661 -0.0606760 -0.2176429 -0.0237858 -0.0845901
0.2660559 0.2055459 -0.3818882 0.1906434 0.4577451 0.1426169
-0.0821414 0.1863512 -0.0756553 0.1301275 -0.1986087 -0.1823989
-0.4602054 0.6986340 -0.3280457 -0.8300334 0.8869824 -0.5905439
0.0087299 -0.1514223 0.0324899 -0.1176028 -0.3914828 0.1398248
0.3118083 -0.2899211 0.0979258 0.2416254 -0.1265985 -0.0048744
-0.9050607 0.0376872 -0.8120661 0.3788349 -0.4995581 0.1471499
-0.4504638 0.2620922 0.1897271 -1.1168104 -0.7273451 0.4873121
-1.2742986 0.5603230 0.3253841 0.3105354 0.2741689 -0.2521501
-0.5023009 1.0333447 -0.4371906 0.1832379 0.4370378 -0.4843458
0.0317661 -0.2445799 -0.1695833 -0.4179328 -1.0664963 0.3591397
1.0611607 -0.1602255 0.0749545 -0.1712037 0.0613705 -0.0815272
-0.7146703 -0.3263894 -1.1492063 -0.8499320 -0.8590925 -1.0760912
-0.3061209 -0.0930516 -0.0569201 -0.5550319 0.7070375 -0.9262022
-0.1955639 0.8334033 -1.0858395 0.1264912 -0.2950562 -0.2529301
0.3595893 1.2914461 0.2017324 -0.2044608 -0.7295697 0.4132364
-0.3346909 -0.2500334 -0.0013693 -0.0794665 1.4128993 0.8559566
-0.7711082 -0.1073988 -0.0352529 -0.1269811 0.4245464 -0.0675674
0.9036640 0.6559532 0.1021075 -0.3420182 -0.2636941 -0.3656088
-0.0237524 -0.1097445 -0.2624289 0.4434040 -0.0353958 -0.6013381
-0.3482173 -0.6471695 -0.3223551 -0.1294751 0.0402732 0.1150647
0.0158367 0.5574550 0.2511401 -0.3075234 0.2382786 0.2764288
-0.2733715 0.5414845 -0.0988475 -0.1136489 0.1051146 0.4676573
-1.0123134 0.4758953 0.0009793 0.0656562 -0.1550449 -0.2637256
-0.9794806 0.0452418 -0.3177382 0.1038971 -0.1037063 -0.4342407
0.2494755 -0.1560635 0.1750024 -0.0332571 -0.0141459 0.7778247
0.1290961 1.1227783 0.6754831 -0.3931763 0.0398014 -0.1083132
0.2475969 -1.0837037 0.3920366 0.4250873 1.3818407 -0.0693531
-0.0713439 0.3560551 0.1940891 -0.2091405 0.7492101 -0.4915692
0.0087676 -0.2243005 -0.3757595 -0.0194615 -0.0176344 -0.2255538
0.1220313 0.1758181 -0.5171374 0.0267208 -0.2325947 -0.5842188
0.1499744 -0.0264810 0.1073537 -0.0863508 0.0671500 0.0420865
0.1877414 0.1677087 0.1405084 0.2638309 -0.0601785 0.0922627
-0.3459806 -0.9508763 0.1018981 0.9806714 1.2114814 -0.3316752
-0.1210378 0.3641824 -0.0428394 -0.1691488 -0.1899077 -0.6911820
-0.4376929 0.6563464 -0.0608971 -0.0896407 -0.1699005 0.1359929
-1.3924785 -0.1627628 -1.5516400 -0.3035085 0.0178200 -1.4863746
0.0438681 0.0484114 0.0270393 -0.0054302 0.0931185 -0.0146426
-0.8905794 0.5164314 0.8067633 -0.1898536 -0.0655096 -0.2182773
-0.9025014 0.3259906 0.7365504 0.4235716 0.0251638 -0.6390186
-0.1767765 0.2016916 -0.0842138 -0.1494476 -0.6076502 -0.0667948
0.2970039 0.4789443 -0.5623290 -0.1093639 -0.0837020 -0.0660676
-0.1534170 0.0846723 -0.8223849 0.1566223 0.0958514 -0.0143775
-0.0747091 0.3602337 -0.5268976 -0.1243490 0.0697870 -0.5864104
-0.7953227 1.2185252 1.5347194 0.0017755 0.1131245 0.0209041
0.6740032 0.2965879 -0.2779385 -0.6654745 0.2273280 -1.8723971
-0.1877536 -0.3626622 -0.0054696 -0.4432080 -0.4117906 -0.0694564
0.1640705 -0.3295369 -0.1418406 -0.2535946 0.2856995 0.0583081
-0.1337134 -0.8456786 -0.7937398 0.5493628 -0.4162892 0.0467339
-0.0428190 -0.1846102 0.3213516 -0.6181366 0.1948042 0.7455271
-0.4628589 0.3608647 -0.6338880 -0.0061963 -0.0313458 -0.0670155
-0.9632936 1.0025894 0.1024932 0.4309240 -0.4412806 0.6282717
-0.0243450 0.1657529 0.2323478 -0.0375354 -0.3257022 -0.1624048
0.0983386 0.4534857 0.3575164 -0.2611314 0.2331125 0.1739410
0.9700266 0.3158933 -1.4549427 0.3307498 -0.7105291 0.4061009
0.2583687 -0.1540749 0.2014267 -0.9578593 -0.1877302 0.0967660
-0.7176219 -0.4735767 -0.1334866 -0.1345810 -0.0024476 -0.1373119
-0.3951243 -0.5842254 -0.2096133 0.4081656 1.1846943 -0.0399308
-0.1482955 0.1542491 -0.2035487 0.0259267 0.2351159 -0.0450485
-0.2236299 -0.0061447 -0.0662322 -0.0600040 0.0658372 0.3862552
0.6335214 -0.2282774 0.2264249 -0.4257476 0.4474521 -0.1079376
0.1986455 -0.3728916 0.1638157 0.1045905 0.2229558 0.2764399
0.0696170 0.0966511 -0.5207998 -0.2099601 -0.0244919 -0.2909304
-0.0263607 0.1668569 -0.0734957 -0.2100428 -0.2602480 -0.1460314
-0.1051211 0.1558527 0.0950602 -0.6368476 0.2308256 0.0255312
0.5169142 0.2814007 0.3949530 0.0856713 0.1771519 0.2749909
-0.0801857 0.1441902 0.2317740 0.4208475 0.2195027 0.3952688
-0.1407218 0.3386750 0.0221568 0.1572310 0.8038444 0.1617810
0.2663948 0.7538431 -1.0149895 0.0296630 0.3019602 -0.2140849
-0.1831251 -0.1282530 -0.3027464 -0.2949555 -0.2742729 -0.8205664
-0.1766186 -0.2607680 0.0950641 -0.5894592 -0.0014744 0.3300837
0.6296114 -0.1474829 0.1154441 0.0719384 -0.0987872 -0.0951834
0.0657346 -0.6435108 -0.2974908 0.7003478 -0.0488745 0.2467209
0.1718352 -0.1614262 0.3303680 0.4376788 -0.2395941 1.6728060
-0.0087944 1.2687445 -0.0398089 -0.1390378 0.0081770 -0.1836541
-0.3834039 -0.7008017 1.0405587 -0.1016404 0.2162828 -0.7360300
-0.0679359 -0.3550573 -0.1323387 0.3473133 0.5866653 -0.1389601
-0.6813921 0.1878975 0.5907121 -0.0308909 0.1800175 -0.0331103
1.1450220 -0.6910050 -0.2963395 -0.9778203 -0.6975230 0.7810171
28.1673595 28.1128021 27.5906638 90.0000000 90.0000000 90.0000000
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wrappers/python/tests/systems/par_all36_prot.prm 0 → 100644
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*>>>> CHARMM36 All-Hydrogen Parameter File for Proteins <<<<<<<<<<
*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<<
*>>>>>>>>>>>>>>>>>>>>>>>>>> Feb. 2012 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
* All comments to the CHARMM web site: www.charmm.org
* parameter set discussion forum
*
!references
!
!Robert B. Best, R.B., Xiao Zhu, X., Shim, J., Lopes, P.
!Mittal, J., Feig, M. and MacKerell, A.D., Jr. Optimization of the
!additive CHARMM all-atom protein force field targeting improved
!sampling of the backbone phi, psi and sidechain chi1 and chi2
!dihedral angles. In preparation
!
!MacKerell, A.D., Jr., Feig, M. and Brooks, III, C.L. "Improved
!treatment of the protein backbone in empirical force fields," Journal
!of the American Chemical Society, 126: 698-699, 2004
!
!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.;
!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.;
!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos,
!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III,
!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.;
!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom
!empirical potential for molecular modeling and dynamics Studies of
!proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616.
ATOMS
MASS 31 H 1.00800 ! polar H
MASS 32 HC 1.00800 ! N-ter H
MASS 33 HA 1.00800 ! nonpolar H
MASS 34 HP 1.00800 ! aromatic H
MASS 35 HB1 1.00800 ! backbone H
MASS 36 HB2 1.00800 ! aliphatic backbone H, to CT2
MASS 37 HR1 1.00800 ! his he1, (+) his HG,HD2
MASS 38 HR2 1.00800 ! (+) his HE1
MASS 39 HR3 1.00800 ! neutral his HG, HD2
MASS 40 HS 1.00800 ! thiol hydrogen
MASS 41 HE1 1.00800 ! for alkene; RHC=CR
MASS 42 HE2 1.00800 ! for alkene; H2C=CR
MASS 43 HA1 1.00800 ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS 44 HA2 1.00800 ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS 45 HA3 1.00800 ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS 46 C 12.01100 ! carbonyl C, peptide backbone
MASS 47 CA 12.01100 ! aromatic C
MASS 48 CT 12.01100 ! aliphatic sp3 C, new LJ params, no hydrogens, see retinol stream file for parameters
MASS 49 CT1 12.01100 ! aliphatic sp3 C for CH
MASS 50 CT2 12.01100 ! aliphatic sp3 C for CH2
MASS 51 CT2A 12.01100 ! from CT2 (GLU, HSP chi1/chi2 fitting) 05282010, zhu
MASS 52 CT3 12.01100 ! aliphatic sp3 C for CH3
MASS 53 CPH1 12.01100 ! his CG and CD2 carbons
MASS 54 CPH2 12.01100 ! his CE1 carbon
MASS 55 CPT 12.01100 ! trp C between rings
MASS 56 CY 12.01100 ! TRP C in pyrrole ring
MASS 57 CP1 12.01100 ! tetrahedral C (proline CA)
MASS 58 CP2 12.01100 ! tetrahedral C (proline CB/CG)
MASS 59 CP3 12.01100 ! tetrahedral C (proline CD)
MASS 60 CC 12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2
MASS 61 CD 12.01100 ! carbonyl C, pres aspp,glup,ct1
MASS 62 CS 12.01100 ! thiolate carbon
MASS 63 CE1 12.01100 ! for alkene; RHC=CR
MASS 64 CE2 12.01100 ! for alkene; H2C=CR
MASS 65 CAI 12.01100 ! aromatic C next to CPT in trp
MASS 66 N 14.00700 ! proline N
MASS 67 NR1 14.00700 ! neutral his protonated ring nitrogen
MASS 68 NR2 14.00700 ! neutral his unprotonated ring nitrogen
MASS 69 NR3 14.00700 ! charged his ring nitrogen
MASS 70 NH1 14.00700 ! peptide nitrogen
MASS 71 NH2 14.00700 ! amide nitrogen
MASS 72 NH3 14.00700 ! ammonium nitrogen
MASS 73 NC2 14.00700 ! guanidinium nitrogen
MASS 74 NY 14.00700 ! TRP N in pyrrole ring
MASS 75 NP 14.00700 ! Proline ring NH2+ (N-terminal)
MASS 76 O 15.99900 ! carbonyl oxygen
MASS 77 OB 15.99900 ! carbonyl oxygen in acetic acid
MASS 78 OC 15.99900 ! carboxylate oxygen
MASS 79 OH1 15.99900 ! hydroxyl oxygen
MASS 80 OS 15.99940 ! ester oxygen
MASS 81 S 32.06000 ! sulphur
MASS 82 SM 32.06000 ! sulfur C-S-S-C type
MASS 83 SS 32.06000 ! thiolate sulfur
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
NH2 CT1 240.000 1.4550 ! From LSN NH2-CT2
!
!Indole/Tryptophan
CA CAI 305.000 1.3750 ! from CA CA
CAI CAI 305.000 1.3750 ! atm, methylindole, fit CCDSS
CPT CA 300.000 1.3600 ! atm, methylindole, fit CCDSS
CPT CAI 300.000 1.3600 ! atm, methylindole, fit CCDSS
CPT CPT 360.000 1.3850 ! atm, methylindole, fit CCDSS
CY CA 350.000 1.3650 ! trj, adm jr., 5/08/91, indole CCDB structure search
CY CAI 350.000 1.3650 ! from CY CA
CY CPT 350.000 1.4300 ! atm, methylindole, fit CDS data
CY CT3 375.000 1.4920 ! atm, methylindole, fit CDS data
CY CT2 375.000 1.4920 ! atm, methylindole, fit CDS data
HP CAI 340.000 1.0800 ! from HP CA
HP CY 350.000 1.0800 ! trp, adm jr., 12/30/91
NY CA 270.000 1.3700 ! trp, adm jr., 12/30/91
NY CPT 270.000 1.3700 ! atm, methylindole, from CCDS 1/17/04
NY H 537.500 0.9760 ! atm, methylindole, 1/17/04
CA CA 305.000 1.3750 ! ALLOW ARO
! benzene, JES 8/25/89
CE1 CE1 440.000 1.3400 !
! for butene; from propene, yin/adm jr., 12/95
CE1 CE2 500.000 1.3420 !
! for propene, yin/adm jr., 12/95
CE1 CT2 365.000 1.5020 !
! for butene; from propene, yin/adm jr., 12/95
CE1 CT3 383.000 1.5040 !
! for butene, yin/adm jr., 12/95
CE2 CE2 510.000 1.3300 !
! for ethene, yin/adm jr., 12/95
CP1 C 250.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP1 CC 250.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP1 CD 200.000 1.4900 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 222.500 1.5270 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP2 222.500 1.5370 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 CP2 222.500 1.5370 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CPH1 CPH1 410.000 1.3600 ! ALLOW ARO
! histidine, adm jr., 6/27/90
CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT1 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT1 CT1 222.500 1.5000 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT2 CA 230.000 1.4900 ! ALLOW ALI ARO
! phe,tyr, JES 8/25/89
CT2 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT2 CPH1 229.630 1.5000 ! ALLOW ARO
! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
CT2 CT1 222.500 1.5380 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 CT2 222.500 1.5300 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
CT3 CA 230.000 1.4900 ! ALLOW ALI ARO
! toluene, adm jr. 3/7/92
CT3 CC 200.000 1.5220 ! ALLOW POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT3 CD 200.000 1.5220 ! ALLOW POL
! adm jr. 5/02/91, acetic acid pure solvent
CT3 CPH1 229.630 1.5000 ! ALLOW ARO
! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
CT3 CS 190.000 1.5310 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
CT3 CT1 222.500 1.5380 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT2 222.500 1.5280 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT3 222.500 1.5300 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
H CD 330.000 1.1100 ! ALLOW PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA1 CC 317.130 1.1000 ! ALLOW POL
! adm jr., 5/13/91, formamide geometry and vibrations
HA2 CP2 309.000 1.1110 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA2 CP3 309.000 1.1110 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA2 CS 300.000 1.1110 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA3 CS 300.000 1.1110 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA1 CT1 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA2 CT2 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA3 CT3 322.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
!HA CY 330.000 1.0800 ! ALLOW ARO
! JWK 05/14/91 new r0 from indole
HE1 CE1 360.500 1.1000 !
! for propene, yin/adm jr., 12/95
HE2 CE2 365.000 1.1000 !
! for ethene, yin/adm jr., 12/95
HB1 CP1 330.000 1.0800 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB1 CT1 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB2 CT2 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
!HB3 CT3 330.000 1.0800 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HP CA 340.000 1.0800 ! ALLOW ARO
! phe,tyr JES 8/25/89
HR1 CPH1 375.000 1.0830 ! ALLOW ARO
! his, adm jr., 6/27/90
HR1 CPH2 340.000 1.0900 ! ALLOW ARO
! his, adm jr., 6/28/29
HR2 CPH2 333.000 1.0700 ! ALLOW ARO
! his, adm jr., 6/27/90
HR3 CPH1 365.000 1.0830 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
N C 260.000 1.3000 ! ALLOW PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 320.000 1.4340 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP3 320.000 1.4550 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC2 C 450.000 1.3650 ! ALLOW PEP POL ARO
! mp2/6-311g** mgua vib. data, adm jr., 1/04
NC2 CT2 390.000 1.4900 ! ALLOW ALI POL
! mp2/6-311g** mgua vib. data, adm jr., 1/04
NC2 CT3 390.000 1.4900 ! ALLOW ALI POL
! mp2/6-311g** mgua vib. data, adm jr., 1/04
NC2 HC 455.000 1.0000 ! ALLOW POL
! 405.0->455.0 GUANIDINIUM (KK)
NH1 C 370.000 1.3450 ! ALLOW PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 320.000 1.4300 ! ALLOW ALI PEP POL ARO
! NMA Gas & Liquid Phase IR Spectra (LK)
NH1 CT2 320.000 1.4300 ! ALLOW ALI PEP POL ARO
! NMA Gas & Liquid Phase IR Spectra (LK)
NH1 CT3 320.000 1.4300 ! ALLOW ALI PEP POL ARO
! NMA Gas & Liquid Phase IR Spectra (LK)
NH1 H 440.000 0.9970 ! ALLOW PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 HC 405.000 0.9800 ! ALLOW PEP POL ARO
! (DS)
NH2 CC 430.000 1.3600 ! ALLOW PEP POL ARO
! adm jr. 4/10/91, acetamide
NH2 CT2 240.000 1.4550
! from NH2 CT3, neutral glycine, adm jr.
NH2 CT3 240.000 1.4550 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
NH2 H 480.000 1.0000 ! ALLOW POL
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 HC 460.000 1.0000 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
NH3 CT1 200.000 1.4800 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 CT2 200.000 1.4800 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 CT3 200.000 1.4800 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 HC 403.000 1.0400 ! ALLOW POL
! new stretch and bend; methylammonium (KK 03/10/92)
NP CP1 320.000 1.4850 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP3 320.000 1.5020 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP HC 460.000 1.0060 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NR1 CPH1 400.000 1.3800 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR1 CPH2 400.000 1.3600 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR1 H 466.000 1.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 CPH1 400.000 1.3800 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 CPH2 400.000 1.3200 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR3 CPH1 380.000 1.3700 ! ALLOW ARO
! his, adm jr., 6/28/90
NR3 CPH2 380.000 1.3200 ! ALLOW ARO
! his, adm jr., 6/27/90
NR3 H 453.000 1.0000 ! ALLOW ARO
! his, adm jr., 6/27/90
O C 620.000 1.2300 ! ALLOW PEP POL ARO
! Peptide geometry, condensed phase (LK)
O CC 650.000 1.2300 ! ALLOW PEP POL ARO
! adm jr. 4/10/91, acetamide
OB CC 750.000 1.2200 ! ALLOW PEP POL ARO
! adm jr., 10/17/90, acetic acid vibrations and geom.
OB CD 750.000 1.2200 ! ALLOW PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
OC CA 525.000 1.2600 ! ALLOW PEP POL ARO ION
! adm jr. 8/27/91, phenoxide
OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION
! adm jr. 7/23/91, acetic acid
OC CT2 450.000 1.3300 ! ALLOW ALC
! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
OC CT3 450.000 1.3300 ! ALLOW ALC
! methoxide 6-31+G* geom/freq, adm jr., 6/1/92
OH1 CA 334.300 1.4110 ! ALLOW ARO ALC
! MeOH, EMB 10/10/89,
OH1 CD 230.000 1.4000 ! ALLOW PEP POL ARO ALC
! adm jr. 5/02/91, acetic acid pure solvent
OH1 CT1 428.000 1.4200 ! ALLOW ALI ALC ARO
! methanol vib fit EMB 11/21/89
OH1 CT2 428.000 1.4200 ! ALLOW ALI ALC ARO
! methanol vib fit EMB 11/21/89
OH1 CT3 428.000 1.4200 ! ALLOW ALI ALC ARO
! methanol vib fit EMB 11/21/89
OH1 H 545.000 0.9600 ! ALLOW ALC ARO
! EMB 11/21/89 methanol vib fit
OS CD 150.000 1.3340 ! ALLOW POL PEP
! adm jr. 5/02/91, acetic acid pure solvent
OS CT3 340.000 1.4300 ! ALLOW POL PEP
! adm jr., 4/05/91, for PRES CT1 from methylacetate
S CT2 198.000 1.8180 ! ALLOW ALI SUL ION
! fitted to C-S s 9/26/92 (FL)
S CT3 240.000 1.8160 ! ALLOW ALI SUL ION
! fitted to C-S s 9/26/92 (FL)
S HS 275.000 1.3250 ! ALLOW SUL ION
! methanethiol pure solvent, adm jr., 6/22/92
SM CT2 214.000 1.8160 ! ALLOW SUL ION
! improved CSSC surface in DMDS 5/15/92 (FL)
SM CT3 214.000 1.8160 ! ALLOW SUL ION
! improved CSSC surface in DMDS 5/15/92 (FL)
SM SM 173.000 2.0290 ! ALLOW SUL ION
! improved CSSC surface in DMDS 5/15/92 (FL)
SS CS 205.000 1.8360 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HR1 CD 330.000 1.1100 ! acetaldehyde, benzaldehyde, 3ALP
O CD 720.000 1.2050 ! acetaldehyde, benzaldehyde, 3ALP. from stream/toppar_all27_na_bkb_modifications.str
CT2A CT1 222.500 1.5380 ! from CT2 CT1, Zhu
CT2 CT2A 222.500 1.5300 ! from CT2 CT2, Zhu
CT2A HA2 309.000 1.1110 ! from HA2 CT2, Zhu
CT2A CPH1 229.630 1.5000 ! from CT2 CPH1, Zhu
!ASP, CT2->CT2A
CT2A CC 200.000 1.5220 ! from CT2 CC, jshim
ANGLES
!
!V(angle) = Ktheta(Theta - Theta0)**2
!
!V(Urey-Bradley) = Kub(S - S0)**2
!
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley)
!S0: A
!
!atom types Ktheta Theta0 Kub S0
!
H NH2 CT1 50.000 111.00 ! From LSN HC-NH2-CT2
NH2 CT1 CT2 67.700 110.00 ! From LSN NH2-CT2-CT2
NH2 CT1 CT3 67.700 110.00 ! From LSN NH2-CT2-CT2
CT1 CD OH1 55.000 110.50 ! From ASPP CT2-CD-OH1
CT3 CT1 CD 52.000 108.00 ! Ala cter
NH2 CT1 HB1 38.000 109.50 50.00 2.1400 ! From LSN NH2-CT2-HA
NH2 CT1 C 50.000 107.00 ! From ALA Dipep. NH1-CT2-C
!
!Indole/Tryptophan
CAI CAI CA 40.000 120.00 35.00 2.41620 ! from CA CA CA
CAI CA CA 40.000 120.00 35.00 2.41620 ! from CA CA CA
CPT CA CA 50.000 113.20 ! atm, methylindole, 1/17/04
CPT CPT CA 50.000 110.00 ! atm, methylindole, 1/17/04
CPT CAI CA 50.000 113.20 ! atm, methylindole, 1/17/04
CPT CPT CAI 50.000 110.00 ! atm, methylindole, 1/17/04
CPT CY CA 85.000 106.40 25.00 2.26100 ! atm, methylindole, 1/17/04
CPT NY CA 85.000 112.00 ! atm, methylindole, 1/17/04
CT2 CY CA 30.000 127.00 ! atm, methylindole, CT3 CY CA
CT2 CY CPT 30.000 126.70 ! atm, methylindole, 1/17/04
CT3 CY CA 30.000 127.00 ! atm, methylindole, CT3 CY CA
CT3 CY CPT 30.000 126.70 ! atm, methylindole, 1/17/04
CY CPT CA 130.000 133.50 ! atm, methylindole, 1/17/04
CY CPT CAI 130.000 133.50 ! atm, methylindole, 1/17/04
CY CPT CPT 85.000 108.00 ! atm, methylindole, 1/17/04
CY CT2 CT1 58.350 114.00 ! from TRP crystal, JWK
CY CT2 CT3 58.350 114.00 ! from TRP crystal, JWK
H NY CA 28.000 126.00 ! trp, adm jr., 12/30/91
H NY CAI 28.000 126.00 ! trp, adm jr., 12/30/91
H NY CPT 28.000 126.00 ! trp, adm jr., 12/30/91
HA2 CT2 CY 55.000 109.50 ! atm, methylindole, 1/17/04
HA3 CT3 CY 55.000 109.50 ! atm, methylindole, 1/17/04
HP CA CAI 30.000 120.00 22.00 2.15250 ! from HP CA CA
HP CAI CA 30.000 120.00 22.00 2.15250 ! from HP CA CA
HP CA CPT 30.000 122.00 22.00 2.14600 ! trp, adm jr., 12/30/91
HP CAI CPT 30.000 122.00 22.00 2.14600 ! from HP CA CPT
HP CA CY 32.000 125.00 25.00 2.17300 ! JWK 05/14/91 new theta0 and r0UB from indole
HP CY CA 32.000 126.40 25.00 2.18600 ! trp, adm jr., 12/30/91
HP CY CPT 32.000 126.40 25.00 2.25500 ! JWK 05/14/91 new theta0 and r0UB from indole
NY CA CY 85.000 110.50 25.00 2.24000 ! trp, adm jr., 12/30/91
NY CA HP 32.000 125.00 25.00 2.17700 ! JWK 05/14/91 new theta0 and r0UB from indole
NY CPT CA 130.000 129.50 ! atm, methylindole, 1/17/04
NY CPT CAI 130.000 129.50 ! atm, methylindole, 1/17/04
NY CPT CPT 95.000 107.40 ! atm, methylindole, 1/17/04
CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO
! JES 8/25/89
CE1 CE1 CT2 48.00 123.50 !
! for 2-butene, yin/adm jr., 12/95
CE1 CE1 CT3 48.00 123.50 !
! for 2-butene, yin/adm jr., 12/95
CE1 CT2 CT3 32.00 112.20 !
! for 1-butene; from propene, yin/adm jr., 12/95
CE2 CE1 CT2 48.00 126.00 !
! for 1-butene; from propene, yin/adm jr., 12/95
CE2 CE1 CT3 47.00 125.20 !
! for propene, yin/adm jr., 12/95
CP1 N C 60.000 117.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 C 52.000 112.3000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 CC 52.000 112.3000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP1 CD 50.000 112.3000 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP2 CP2 CP1 70.000 108.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 CP2 CP2 70.000 108.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 N C 60.000 117.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 N CP1 100.000 114.2000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CP3 NP CP1 100.000 111.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CPH2 NR1 CPH1 130.000 107.5000 ! ALLOW ARO
! his, adm jr., 6/27/90
CPH2 NR2 CPH1 130.000 104.0000 ! ALLOW ARO
! his, adm jr., 6/27/90
CPH2 NR3 CPH1 145.000 108.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
CT1 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
CT1 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 6/27/2012, for Thr with CT1 patch
CT1 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT1 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO
! PARALLH19 (JES)
CT1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT1 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
CT1 CT2 CPH1 58.350 113.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted
CT1 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT1 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
CT2 CA CA 45.800 122.3000 ! ALLOW ALI ARO
! PARALLH19 (JES)
CT2 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS
CT2 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
CT2 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2A CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
CT2 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 CT2 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! from CT2 CT1 C, for lactams, adm jr.
CT2 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT3 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
CT2 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
CT2A CT2 CD 52.000 108.0000 ! for GLUP, ZHU
CT2 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT2 CT2 CT2 58.350 113.60 11.16 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT2 CT3 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT2 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO
! 107.5->120.0 to make planar Arg (KK)
CT2 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
CT2 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP
! adm jr. 5/02/91, acetic acid pure solvent
CT3 CA CA 45.800 122.3000 ! ALLOW ALI ARO
! toluene, adm jr., 3/7/92
CT3 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS
CT3 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/09/92, for ALA cter
CT3 CT1 CT1 53.350 108.50 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT1 CT2 53.350 114.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT1 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO
! ethylbenzene, adm jr., 3/7/92
CT3 CT2 CPH1 58.350 113.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted
CT3 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
CT3 CT2 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 CT2 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
CT3 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO
! methylguanidinium, adm jr., 3/26/92
CT3 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
CT3 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP
! adm jr. 5/02/91, acetic acid pure solvent
CT3 S CT2 34.000 95.0000 ! ALLOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
H NH1 C 34.000 123.0000 ! ALLOW PEP POL ARO
! NMA Vib Modes (LK)
H NH1 CT1 35.000 117.0000 ! ALLOW PEP POL ARO ALI
! NMA Vibrational Modes (LK)
H NH1 CT2 35.000 117.0000 ! ALLOW PEP POL ARO ALI
! NMA Vibrational Modes (LK)
H NH1 CT3 35.000 117.0000 ! ALLOW PEP POL ARO ALI
! NMA Vibrational Modes (LK)
H NH2 CC 50.000 120.0000 ! ALLOW POL PEP ARO
! his, adm jr. 8/13/90 acetamide geometry and vibrations
H NH2 H 23.000 120.0000 ! ALLOW POL
! adm jr. 8/13/90 acetamide geometry and vibrations
H NR1 CPH1 30.000 125.50 20.00 2.15000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NR1 CPH2 30.000 127.00 20.00 2.14000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NR3 CPH1 25.000 126.00 15.00 2.13000 ! ALLOW ARO
! his, adm jr., 6/27/90
H NR3 CPH2 25.000 126.00 15.00 2.09000 ! ALLOW ARO
! his, adm jr., 6/27/90
H OH1 CA 65.000 108.0000 ! ALLOW ALC ARO
! JES 8/25/89 phenol
H OH1 CD 55.000 115.0000 ! ALLOW ALC ARO PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
H OH1 CT1 57.500 106.0000 ! ALLOW ALC ARO ALI
! methanol vib fit EMB 11/21/89
H OH1 CT2 57.500 106.0000 ! ALLOW ALC ARO ALI
! methanol vib fit EMB 11/21/89
H OH1 CT3 57.500 106.0000 ! ALLOW ALC ARO ALI
! methanol vib fit EMB 11/21/89
HA2 CP2 CP1 33.430 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA2 CP2 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA2 CP2 CP3 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA2 CP2 HA2 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA2 CP3 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA2 CP3 HA2 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA2 CS CT3 34.600 110.10 22.53 2.17900 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA2 CS HA2 35.500 108.40 14.00 1.77500 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA3 CS HA3 35.500 108.40 14.00 1.77500 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA1 CT1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA1 CT1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA1 CT1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA1 CT1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA1 CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA1 CT1 HA1 35.500 109.00 5.40 1.80200 ! TEST for test cpd
! based on HA CT2 HA
HA2 CT2 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA2 CT2 CA 49.300 107.5000 ! ALLOW ALI ARO
! PARALLH19 (JES)
HA2 CT2 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HA2 CT2 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA2 CT2 CE1 45.00 111.50 !
! for 1-butene; from propene, yin/adm jr., 12/95
HA2 CT2 CPH1 33.430 109.5000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
HA2 CT2 CT1 26.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
HA2 CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA2 CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA2 CT2 HA2 35.500 109.00 5.40 1.80200 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA3 CT3 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! alanine dipeptide, LK, replaced, adm jr., 5/09/91
HA3 CT3 CA 49.300 107.5000 ! ALLOW ALI ARO
! toluene, adm jr. 3/7/92
HA3 CT3 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HA3 CT3 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
HA3 CT3 CE1 42.00 111.50 !
! for 2-butene, yin/adm jr., 12/95
HA3 CT3 CPH1 33.430 109.5000 ! ALLOW ARO
! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
HA3 CT3 CS 34.600 110.10 22.53 2.17900 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA3 CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI
! alkane frequencies (MJF), alkane geometries (SF)
HA3 CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA3 CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA3 CT3 HA3 35.500 108.40 5.40 1.80200 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HE1 CE1 CE1 52.00 119.50 !
! for 2-butene, yin/adm jr., 12/95
HE1 CE1 CE2 42.00 118.00 !
! for propene, yin/adm jr., 12/95
HE1 CE1 CT2 40.00 116.00 !
! for 1-butene; from propene, yin/adm jr., 12/95
HE1 CE1 CT3 22.00 117.00 !
! for propene, yin/adm jr., 12/95
HE2 CE2 CE1 45.00 120.50 !
! for propene, yin/adm jr., 12/95
HE2 CE2 CE2 55.50 120.50 !
! for ethene, yin/adm jr., 12/95
HE2 CE2 HE2 19.00 119.00 !
! for propene, yin/adm jr., 12/95
HB1 CP1 C 50.000 112.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB1 CP1 CC 50.000 112.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB1 CP1 CD 50.000 112.0000 ! ALLOW PEP POL PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB1 CP1 CP2 35.000 118.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB1 CT1 C 50.000 109.5000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB1 CT1 CC 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HB1 CT1 CD 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
HB1 CT1 CT1 35.000 111.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB1 CT1 CT2 35.000 111.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB1 CT1 CT3 35.000 111.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB2 CT2 C 50.000 109.5000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB2 CT2 CC 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
HB2 CT2 CD 50.000 109.5000 ! ALLOW PEP POL
! adm jr. 5/02/91, acetic acid pure solvent
HB2 CT2 HB2 36.000 115.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HC NC2 C 49.000 120.0000 ! ALLOW POL PEP ARO
! 35.3->49.0 GUANIDINIUM (KK)
HC NC2 CT2 40.400 120.0000 ! ALLOW POL ALI
! 107.5->120.0 to make planar Arg (KK)
HC NC2 CT3 40.400 120.0000 ! ALLOW POL ALI
! methylguanidinium, adm jr., 3/26/92
HC NC2 HC 25.000 120.0000 ! ALLOW POL
! 40.0->25.0 GUANIDINIUM (KK)
HC NH2 CT2 50.000 111.0000 ! ALLOW POL
! from HC NH2 CT3, neutral glycine, adm jr.
HC NH2 CT3 50.000 111.0000 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
HC NH2 HC 39.000 106.5000 ! ALLOW POL
! 40.0->25.0 GUANIDINIUM (KK)
HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
! new stretch and bend; methylammonium (KK 03/10/92)
HC NH3 CT2 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
! new stretch and bend; methylammonium (KK 03/10/92)
HC NH3 CT3 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
! new stretch and bend; methylammonium (KK 03/10/92)
HC NH3 HC 44.000 109.5000 ! ALLOW POL
! new stretch and bend; methylammonium (KK 03/10/92)
HC NP CP1 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HC NP CP3 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HC NP HC 51.000 107.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HP CA CA 30.000 120.00 22.00 2.15250 ! ALLOW ARO
! JES 8/25/89 benzene
HR1 CPH1 CPH1 22.000 130.00 15.00 2.21500 ! ALLOW ARO
! adm jr., 6/27/90, his
HR3 CPH1 CPH1 25.000 130.00 20.00 2.20000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HS S CT2 38.800 95.0000 ! ALLOW SUL ION ALI
! methanethiol pure solvent, adm jr., 6/22/92
HS S CT3 43.000 95.0000 ! ALLOW SUL ION ALI
! methanethiol pure solvent, adm jr., 6/22/92
N C CP1 20.000 112.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT1 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT2 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT3 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 C 50.000 108.2000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 CC 50.000 108.2000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 CD 50.000 108.2000 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 CP2 70.000 110.8000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP1 HB1 48.000 112.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP3 CP2 70.000 110.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N CP3 HA2 48.000 108.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC2 C NC2 40.000 120.00 70.00 2.31
! mp2/6-311g** mgua vib data, adm jr., 1/04
! N-N distances: 2.29001, 2.31146, 2.33240
NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL
! arg, (DS)
NC2 CT2 HA2 56.500 107.5000 ! ALLOW ALI POL
! mp2/6-311g** mgua vib data, adm jr., 1/04
NC2 CT3 HA3 56.5000 107.5000 ! ALLOW ALI POL
! mp2/6-311g** mgua vib data, adm jr., 1/04
NH1 C CP1 80.000 116.5000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH1 C CT1 80.000 116.5000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
NH1 C CT2 80.000 116.5000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
NH1 C CT3 80.000 116.5000 ! ALLOW ALI PEP POL ARO
! NMA Vib Modes (LK)
NH1 CT1 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
NH1 CT1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 5/02/91, acetic acid pure solvent
NH1 CT1 CT1 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT1 HB1 48.000 108.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT2 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT2 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 5/20/92, for asn,asp,gln,glu and cters
NH1 CT2 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 5/02/91, acetic acid pure solvent
NH1 CT2 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO
! from NH1 CT1 CT2, for lactams, adm jr.
NH1 CT2 HA2 51.500 109.5000 ! ALLOW ALI PEP POL ARO
! from NH1 CT3 HA, for lactams, adm jr.
NH1 CT2 HB2 48.000 108.0000 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
NH1 CT3 HA3 51.500 109.5000 ! ALLOW ALI PEP POL ARO
! NMA crystal (JCS)
NH2 CC CP1 80.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH2 CC CT1 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 CC CT3 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
! adm jr. 8/13/90 acetamide geometry and vibrations
NH2 CC HA1 44.000 111.00 50.00 1.98000 ! ALLOW POL
! adm jr., 5/13/91, formamide geometry and vibrations
NH2 CT2 HB2 38.000 109.50 50.00 2.14000
!from NH2 CT3 HA, neutral glycine, adm jr.
NH2 CT2 CD 52.000 108.0000
!from CT2 CT2 CD, neutral glycine, adm jr.
NH2 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL
!from NH3 CT2 CT2, neutral lysine
NH2 CT2 HA2 38.000 109.50 50.00 2.14000
!from NH2 CT3 HA, neutral lysine
NH2 CT3 HA3 38.000 109.50 50.00 2.14000 ! ALLOW POL
! methylamine geom/freq, adm jr., 6/2/92
NH3 CT1 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI
! new aliphatics, adm jr., 2/3/92
NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
NH3 CT1 CT1 67.700 110.0000 ! ALLOW ALI POL
! new aliphatics, adm jr., 2/3/92
NH3 CT1 CT2 67.700 110.0000 ! ALLOW ALI POL
! new aliphatics, adm jr., 2/3/92
NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL
! new aliphatics, adm jr., 2/3/92
NH3 CT1 HB1 51.500 107.5000 ! ALLOW ALI POL PEP
! new aliphatics, adm jr., 2/3/92
NH3 CT2 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI
! alanine (JCS)
NH3 CT2 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 4/05/91, for asn,asp,gln,glu and cters
NH3 CT2 CD 43.700 110.0000 ! ALLOW PEP POL ARO ALI
! adm jr. 5/02/91, acetic acid pure solvent
NH3 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL
! methylammonium
NH3 CT2 CT3 67.700 110.0000 ! ALLOW ALI POL
! ethylammonium
NH3 CT2 HA2 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NH3 CT2 HB2 51.500 107.5000 ! ALLOW ALI POL PEP
! for use on NTER -- from NH3 CT2HA (JCS) -- (LK)
NH3 CT3 HA3 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL
! new stretch and bend; methylammonium (KK 03/10/92)
NP CP1 C 50.000 106.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP1 CC 50.000 106.0000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP1 CD 50.000 106.0000 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP1 CP2 70.000 108.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP1 HB1 51.500 107.5000 ! ALLOW ALI POL PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP3 CP2 70.000 108.5000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NP CP3 HA2 51.500 109.1500 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NR1 CPH1 CPH1 130.000 106.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR1 CPH1 CT2 45.800 124.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC FROM CA CT2CT
NR1 CPH1 CT3 45.800 124.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC FROM CA CT2CT
NR1 CPH1 HR3 25.000 124.00 20.00 2.14000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
NR1 CPH2 HR1 25.000 122.50 20.00 2.14000 ! ALLOW ARO
! his, adm jr., 6/27/90
NR2 CPH1 CPH1 130.000 110.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR2 CPH1 CT2 45.800 120.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC FROM CA CT2CT
NR2 CPH1 HR3 25.000 120.00 20.00 2.14000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
NR2 CPH2 HR1 25.000 125.00 20.00 2.12000 ! ALLOW ARO
! his, adm jr., 6/27/90
NR2 CPH2 NR1 130.000 112.5000 ! ALLOW ARO
! his, adm jr., 6/27/90
NR3 CPH1 CPH1 145.000 108.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
NR3 CPH1 CT2 45.800 122.0000 ! ALLOW ARO
! his, ADM JR., 7/22/89, FC FROM CA CT2CT
NR3 CPH1 HR1 22.000 122.00 15.00 2.18000 ! ALLOW ARO
! his, adm jr., 6/27/90
NR3 CPH2 HR2 32.000 126.00 25.00 2.14000 ! ALLOW ARO
! his, adm jr., 6/27/90
NR3 CPH2 NR3 145.000 108.0000 ! ALLOW ARO
! his, ADM JR., 7/20/89
O C CP1 80.000 118.0000 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O C CT1 80.000 121.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
O C CT2 80.000 121.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
O C CT3 80.000 121.0000 ! ALLOW ALI PEP POL ARO
! Alanine Dipeptide ab initio calc's (LK)
O C H 50.000 121.7000 ! ALLOW PEP POL ARO
! acetaldehyde (JCS)
O C N 80.000 122.5000 ! ALLOW PRO PEP POL ARO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O C NH1 80.000 122.5000 ! ALLOW PEP POL ARO
! NMA Vib Modes (LK)
O CC CP1 80.000 118.0000 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O CC CT1 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/10/91, acetamide update
O CC CT2 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/10/91, acetamide update
O CC CT3 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO
! adm jr. 4/10/91, acetamide update
O CC HA1 44.000 122.0000 ! ALLOW POL
! adm jr., 5/13/91, formamide geometry and vibrations
O CC NH2 75.000 122.50 50.00 2.37000 ! ALLOW POL PEP ARO
! adm jr. 4/10/91, acetamide update
OB CD CP1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
OB CD CT1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
OB CD CT2 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
OB CD CT3 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO
! adm jr. 5/02/91, acetic acid pure solvent
OC CA CA 40.000 120.0000 ! ALLOW POL ARO
! adm jr. 8/27/91, phenoxide
OC CC CP1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION
! adm jr. 7/23/91, correction, ACETATE (KK)
OC CC CT2 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION
! adm jr. 7/23/91, correction, ACETATE (KK)
OC CC CT3 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION
! adm jr. 7/23/91, correction, ACETATE (KK)
OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO
! adm jr. 7/23/91, correction, ACETATE (KK)
OC CT2 CT3 65.000 122.0000 ! ALLOW ALC
! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
OC CT2 HA2 65.000 118.3000 ! ALLOW ALC
! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
OC CT3 HA3 65.000 118.3000 ! ALLOW ALC
! methoxide 6-31+G* geom/freq, adm jr., 6/1/92
OH1 CA CA 45.200 120.0000 ! ALLOW ARO ALC
! PARALLH19 WITH [122.3] (JES)
OH1 CD CT2 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC
! adm jr, 10/17/90, acetic acid vibrations
OH1 CD CT3 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC
! adm jr, 10/17/90, acetic acid vibrations
OH1 CD OB 50.000 123.00 210.00 2.26200 ! ALLOW PEP POL ARO ALC
! adm jr, 10/17/90, acetic acid vibrations
OH1 CT1 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT1 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT1 HA1 45.900 108.8900 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT2 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT2 CT2 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT2 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT2 HA2 45.900 108.8900 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OH1 CT3 HA3 45.900 108.8900 ! ALLOW ALI ALC ARO
! MeOH, EMB, 10/10/89
OS CD CP1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
OS CD CT1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP
! adm jr., 4/05/91, for PRES CT1 from methylacetate
OS CD CT2 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP
! adm jr., 4/05/91, for PRES CT1 from methylacetate
OS CD CT3 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP
! adm jr., 4/05/91, for PRES CT1 from methylacetate
OS CD OB 90.000 125.90 160.00 2.25760 ! ALLOW PEP POL
! adm jr. 3/19/92, from lipid methyl acetate
OS CT2 HA2 60.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for PRES CT1 from methyl acetate
OS CT3 HA3 60.000 109.5000 ! ALLOW PEP POL
! adm jr. 4/05/91, for PRES CT1 from methyl acetate
S CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION
! as in expt.MeEtS & DALC crystal, 5/15/92
S CT2 CT2 58.000 114.5000 ! ALLOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
S CT2 CT3 58.000 114.5000 ! ALLOW ALI SUL ION
! expt. MeEtS, 3/26/92 (FL)
S CT2 HA2 46.100 111.3000 ! ALLOW ALI SUL ION
! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90
S CT3 HA3 46.100 111.3000 ! ALLOW ALI SUL ION
! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90
SM CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION
! as in expt.MeEtS & DALC crystal, 5/15/92
SM CT2 CT3 58.000 112.5000 ! ALLOW ALI SUL ION
! diethyldisulfide, as in expt.MeEtS & DALC crystal, 5/15/92
SM CT2 HA2 38.000 111.0000 ! ALLOW ALI SUL ION
! new S-S atom type 8/24/90
SM CT3 HA3 38.000 111.0000 ! ALLOW ALI SUL ION
! new S-S atom type 8/24/90
SM SM CT2 72.500 103.3000 ! ALLOW ALI SUL ION
! expt. dimethyldisulfide, 3/26/92 (FL)
SM SM CT3 72.500 103.3000 ! ALLOW ALI SUL ION
! expt. dimethyldisulfide, 3/26/92 (FL)
SS CS CT3 55.000 118.0000 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
SS CS HA2 40.000 112.3000 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
SS CS HA3 40.000 112.3000 ! ALLOW SUL
! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
O CD HR1 75.000 121.0000 ! acetaldehyde, benzaldehyde, 3ALP, retinal
!For GLU/HSP, Zhu
NH1 CT1 CT2A 70.000 113.5000 ! from NH1 CT1 CT2
HB1 CT1 CT2A 35.000 111.0000 ! from HB1 CT1 CT2
CT2A CT1 C 52.000 108.0000 ! from CT2 CT1 C
CT1 CT2A HA2 26.500 110.1000 22.53 2.17900 ! from HA2 CT2 CT1
CT1 CT2A CT2 58.350 113.5000 11.16 2.56100 ! from CT2 CT2 CT1
HA2 CT2A HA2 35.500 109.0000 5.40 1.80200 ! from HA2 CT2 HA2
HA2 CT2A CT2 26.500 110.1000 22.53 2.17900 ! from HA2 CT2 CT2
CT2A CT2 HA2 26.500 110.1000 22.53 2.17900 ! from HA2 CT2 CT2
CT2A CT2 CC 52.000 108.0000 ! from CT2 CT2 CC
CT1 CT2A CPH1 58.350 113.0000 ! from CT1 CT2 CPH1
HA2 CT2A CPH1 33.430 109.5000 ! from HA2 CT2 CPH1
CT2A CPH1 CPH1 45.800 130.0000 ! from CT2 CPH1 CPH1
CT2A CPH1 NR3 45.800 122.0000 ! from NR3 CPH1 CT2
!ASP, CT2->CT2A, jshim
CT1 CT2A CC 52.000 108.0000 ! from CT1 CT2 CC
HA2 CT2A CC 33.000 109.50 30.00 2.16300 ! from HA2 CT2 CC
OC CC CT2A 40.000 118.00 50.00 2.38800 ! from OC CC CT2
NH3 CT1 CT2A 67.700 110.0000 ! from NH3 CT1 CT2
CT2A CT1 CD 52.000 108.0000 ! from CT2 CT1 CD
DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types Kchi n delta
!
!Neutral N terminus
NH2 CT1 C O 0.0000 1 0.00
NH2 CT1 C NH1 0.0000 1 0.00
H NH2 CT1 CT1 0.0000 1 0.00
H NH2 CT1 C 0.0000 1 0.00
H NH2 CT1 HB1 0.1100 3 0.00 ! From LSN HC-NH2-CT2-HA
H NH2 CT1 CT2 0.1100 3 0.00 ! From LSN HC-NH2-CT2-CT2
H NH2 CT1 CT3 0.1100 3 0.00 ! From LSN HC-NH2-CT2-CT2
!Indole/Tryptophan
CAI CA CA CAI 3.1000 2 180.00 ! from CA CA CA CA
CA CPT CPT CA 3.0000 2 180.00 ! atm, methylindole, 1/17/04
CAI CPT CPT CAI 3.0000 2 180.00 ! atm, methylindole, 1/17/04
CA CY CPT CA 3.0000 2 180.00 ! atm, methylindole, 1/17/04
CA CY CPT CAI 3.0000 2 180.00 ! atm, methylindole, 1/17/04
CA NY CPT CA 3.0000 2 180.00 ! atm, methylindole, 1/17/04
CPT CA CA CA 3.0000 2 180.00 ! JWK 05/14/91 fit to indole
CPT CPT CA CA 3.0000 2 180.00 ! JWK 05/14/91 fit to indole
CA NY CPT CAI 3.0000 2 180.00 ! atm, methylindole, 1/17/04
CPT CAI CA CA 3.0000 2 180.00 ! JWK 05/14/91 fit to indole
CPT CPT CAI CA 3.0000 2 180.00 ! JWK 05/14/91 fit to indole
CPT CPT CY CA 5.0000 2 180.00 ! atm, methylindole, 1/17/04
CPT CPT NY CA 6.5000 2 180.00 ! atm, methylindole, 1/17/04
CT3 CY CPT CA 2.5000 2 180.00 ! atm, methylindole, r6r5
CT3 CY CPT CAI 2.5000 2 180.00 ! atm, methylindole, r6r5
CT3 CY CPT CPT 3.0000 2 180.00 ! atm, methylindole, meth
CT2 CY CPT CA 2.5000 2 180.00 ! atm, methylindole, r6r5
CT2 CY CPT CAI 2.5000 2 180.00 ! atm, methylindole, r6r5
CT2 CY CPT CPT 3.0000 2 180.00 ! atm, methylindole, meth
CY CA NY CPT 6.0000 2 180.00 ! atm, methylindole, 1/17/04
CY CPT CA CA 4.0000 2 180.00 ! atm, methylindole, 1/17/04
CY CPT CPT CA 4.0000 2 180.00 ! atm, methylindole, 1/17/04
CY CPT CAI CA 4.0000 2 180.00 ! atm, methylindole, 1/17/04
CY CPT CPT CAI 4.0000 2 180.00 ! atm, methylindole, 1/17/04
H NY CA CY 0.0500 2 180.00 ! atm, methylindole, 1/17/04
H NY CPT CA 0.2000 2 180.00 ! atm, methylindole, 1/17/04
H NY CPT CAI 0.2000 2 180.00 ! atm, methylindole, 1/17/04
H NY CPT CPT 0.8500 2 180.00 ! atm, methylindole, 1/17/04
HP CAI CA CA 4.2000 2 180.00 ! from HP CA CA CA
HP CA CA CPT 3.0000 2 180.00 ! JWK 05/14/91 fit to indole
HP CA CPT CPT 3.0000 2 180.00 ! JWK indole 05/14/91
HP CA CPT CY 4.0000 2 180.00 ! atm, methylindole, 1/17/04
HP CA CA CAI 4.2000 2 180.00 ! from HP CA CA CA
HP CA CAI CPT 3.0000 2 180.00 ! from HP CA CA CPT
HP CAI CA HP 2.4000 2 180.00 ! from HP CA CA HP
HP CAI CPT CPT 3.0000 2 180.00 ! from HP CA CPT CPT
HP CAI CPT CY 4.0000 2 180.00 ! from HP CA CPT CY, r6r5
HP CA CY CPT 2.8000 2 180.00 ! adm jr., 12/30/91, for jwk
HP CA CY CT3 1.2000 2 180.00 ! atm, methylindole
HP CA CY CT2 1.2000 2 180.00 ! atm, methylindole
HP CA NY CPT 2.6000 2 180.00 ! adm jr., 12/30/91, for jwk
HP CA NY H 0.4000 2 180.00 ! JWK 05/14/91 fit to indole
HP CY CA HP 1.0000 2 180.00 ! JWK 05/14/91 fit to indole
HP CY CPT CA 2.8000 2 180.00 ! JWK 05/14/91 fit to indole
HP CY CPT CAI 2.8000 2 180.00 ! JWK 05/14/91 fit to indole
HP CY CPT CPT 2.6000 2 180.00 ! JWK 05/14/91 fit to indole
NY CA CY CPT 5.0000 2 180.00 ! atm, methylindole, 1/17/04
NY CA CY CT3 2.5000 2 180.00 ! atm, methylindole, from NY CA CY CT3
NY CA CY CT2 2.5000 2 180.00 ! atm, methylindole, from NY CA CY CT3
NY CA CY HP 3.5000 2 180.00 ! JWK indole 05/14/91
NY CPT CA CA 3.0000 2 180.00 ! atm, methylindole, 1/17/04, r6r5
NY CPT CA HP 3.0000 2 180.00 ! JWK 05/14/91 fit to indole, r6r5
NY CPT CPT CA 4.0000 2 180.00 ! atm, methylindole, 1/17/04, bfly
NY CPT CAI CA 3.0000 2 180.00 ! atm, methylindole, 1/17/04
NY CPT CAI HP 3.0000 2 180.00 ! JWK 05/14/91 fit to indole, r6r5
NY CPT CPT CAI 4.0000 2 180.00 ! atm, methylindole, 1/17/04, bfly
NY CPT CPT CY 6.5000 2 180.00 ! JWK 05/14/91 fit to indole, r5 t1
CT3 CT2 CY CA 0.3800 2 0.00 ! trp, from ethylbenzene, adm jr., 3/7/92
CT3 CT2 CY CPT 0.2500 2 180.00 ! atm 1/14/04 3-ethylindole
CT3 CT2 CY CPT 0.3000 3 0.00 ! atm 1/14/04 3-ethylindole
HA3 CT3 CY CA 0.0100 3 0.00 ! atm, methylindole, 1/17/04
HA3 CT3 CY CPT 0.2000 3 0.00 ! atm, methylindole, 1/17/04
HA2 CT2 CY CA 0.0100 3 0.00 ! atm, methylindole, 1/17/04
HA2 CT2 CY CPT 0.2000 3 0.00 ! atm, methylindole, 1/17/04
X CS SS X 0.0000 3 0.20 ! guess
!from methanethiol, HS S CT3 HA
!adm jr., 7/01
C CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP
! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
C CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP
! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
C N CP1 C 0.8000 3 0.00 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CA CA CA CA 3.1000 2 180.00 ! ALLOW ARO
! JES 8/25/89
!CA CT2 CT1 C 0.0400 3 0.00 ! ALLOW ARO
! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
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
CC CT2 NH1 C 2.0000 1 180.00 ! ALLOW PEP POL
! Based on Gly3 data from graf et al, RB 7/1/11
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
CD CT2 NH1 C 2.0000 1 180.00 ! ALLOW PEP POL
! Based on Gly3 data from graf et al, RB 7/1/11
CE1 CE1 CT3 HA3 0.0300 3 0.00 !
! for butene, yin/adm jr., 12/95
CE2 CE1 CT2 CT3 0.5000 1 180.00 !
! 1-butene, adm jr., 2/00 update
CE2 CE1 CT2 CT3 1.3000 3 180.00 !
! 1-butene, adm jr., 2/00 update
CE2 CE1 CT2 HA2 0.1200 3 0.00 !
! for butene, yin/adm jr., 12/95
CE2 CE1 CT3 HA3 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
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 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
!aliphatic chain parameters compatible with the revised side-chain parameters, from all22_carb>>all27_lip>>all31
! lower butane gauche conformer
CT2 CT2 CT2 CT2 0.10 2 180.00 ! alkane, 4/98, adm jr.
CT2 CT2 CT2 CT2 0.15 4 0.00 ! alkane, 4/98, adm jr.
CT2 CT2 CT2 CT2 0.10 6 180.00 ! alkane, 4/98, adm jr.
CT2 CT2 CT2 CT3 0.10 2 180.00 ! alkane, 4/98, adm jr.
CT2 CT2 CT2 CT3 0.15 4 0.00 ! alkane, 4/98, adm jr.
CT2 CT2 CT2 CT3 0.10 6 180.00 ! alkane, 4/98, adm jr.
!
CT2 CT2 NH1 C 1.8000 1 0.00 ! ALLOW PEP
! from CT2 CT1 NH1 C, for lactams, adm jr.
CT2 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT2 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT2 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP
! Revised to adjust NMA cis/trans energy difference. (LK)
CT2 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
CT2 SM SM CT2 1.0000 1 0.00 ! ALLOW ALI SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
CT2 SM SM CT2 4.1000 2 0.00 ! ALLOW ALI SUL ION
! mp 6-311G** dimethyldisulfide, 3/26/92 (FL)
CT2 SM SM CT2 0.9000 3 0.00 ! ALLOW ALI SUL ION
! improved CSSC dihedral in DMDS 5/15/92 (FL)
CT3 C N CP1 2.7500 2 180.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT3 C N CP1 0.3000 4 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT3 C N CP3 2.7500 2 180.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT3 C N CP3 0.3000 4 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
CT3 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP
! Revised to adjust NMA cis/trans energy difference. (LK)
CT3 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
CT3 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP
! for acetylated GLY N-terminus, adm jr.
CT3 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP
! for acetylated GLY N-terminus, adm jr.
CT3 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP
! Revised to adjust NMA cis/trans energy difference. (LK)
CT3 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP
! Gives appropriate NMA cis/trans barrier. (LK)
CT3 CA CA CA 3.1000 2 180.00 ! ALLOW ARO
! toluene, adm jr., 3/7/92
CT3 CE1 CE2 HE2 5.2000 2 180.00 !
! for propene, yin/adm jr., 12/95
CT3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO
! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2
CT3 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP
! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
CT3 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI
! ethylbenzene ethyl rotation, adm jr. 3/7/92
CT3 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO
! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CT3 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO
! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CT3 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
CT3 CT2 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)
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 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 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 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
HA1 CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL
! adm jr. 4/10/91, acetamide update
HA2 CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA2 CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA2 CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HA1 CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
HA2 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89
HA2 CT2 NH1 C 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
HA2 CT2 NH1 H 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
HA2 CT2 S CT3 0.2800 3 0.00 ! ALLOW ALI SUL ION
! DTN 8/24/90
HA3 CT3 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89
HA3 CT3 CS HA2 0.1600 3 0.00 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA3 CT3 CS HA3 0.1600 3 0.00 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
HA3 CT3 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
HA3 CT3 NH1 C 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
HA3 CT3 NH1 H 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
HA3 CT3 S CT2 0.2800 3 0.00 ! ALLOW ALI SUL ION
! DTN 8/24/90
HE1 CE1 CE1 HE1 1.0000 2 180.00 !
! 2-butene, adm jr., 8/98 update
CT3 CE1 CE1 HE1 1.0000 2 180.00 !
! 2-butene, adm jr., 8/98 update
HE1 CE1 CE2 HE2 5.2000 2 180.00 !
! for propene, yin/adm jr., 12/95
HE1 CE1 CT2 HA2 0.0000 3 0.00
! butene, adm jr., 2/00 update
HE1 CE1 CT2 CT3 0.1200 3 0.00 !
! for butene, yin/adm jr., 12/95
HE1 CE1 CT3 HA3 0.0000 3 0.00
! butene, adm jr., 2/00 update
HE2 CE2 CE1 CT2 5.2000 2 180.00 !
! for butene, yin/adm jr., 12/95
HB1 CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB1 CP1 N CP3 0.1000 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB1 CP1 NP CP3 0.0800 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
HB1 CT1 NH1 C 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB1 CT1 NH1 H 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB2 CT2 NH1 C 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HB2 CT2 NH1 H 0.0000 1 0.00 ! ALLOW PEP
! Alanine Dipeptide ab initio calc's (LK)
HC NH2 CT2 HB2 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 NH2 CT2 CT2 0.1100 3 0.00
!from X CT3 NH2 X, neutral lysine
HC NH2 CT2 HA2 0.1100 3 0.00
!from X CT3 NH2 X, neutral lysine
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 HB1 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 HA2 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 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
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 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 HA2 0.2000 3 0.00 ! ALLOW ALI SUL ION
! methanethiol pure solvent, adm jr., 6/22/92
HS S CT3 HA3 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 HB1 0.4000 1 180.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CP1 HB1 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 HB1 0.0000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT2 HB2 0.0000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
N C CT3 HA3 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 HB1 0.4000 1 180.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH1 C CP1 HB1 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 HB1 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 HA2 0.0000 3 0.00 ! ALLOW PEP
! LK for autogenerate dihe, sp2-methyl, no dihedral potential
NH1 C CT2 HB2 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 HA3 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 HB1 0.4000 1 180.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NH2 CC CP1 HB1 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 HA2 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 C NH1 1.0000 1 0.00 ! ALLOW PEP PRO
! RB 1/07/11, based on graf et al Gly 3 N-ter J-couplings 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 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 HA2 0.1900 3 0.00 ! ALLOW ARO
! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
NR1 CPH1 CT3 HA3 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 HA2 0.1900 3 0.00 ! ALLOW ARO
! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
NR2 CPH1 CT3 HA3 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 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 HA2 0.1900 3 0.00 ! ALLOW ARO
! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
NR3 CPH1 CT3 HA3 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
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 HB1 0.4000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O C CP1 HB1 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 HB1 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 HA2 0.0000 3 180.00 ! ALLOW POL
! adm jr., 8/13/90 acetamide geometry and vibrations
O C CT2 HB2 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 HA3 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 HB1 0.4000 1 0.00 ! ALLOW PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
O CC CP1 HB1 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 HA2 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 HB1 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 HA2 0.0100 3 0.00 ! ALLOW ALI SUL ION
! DTN 8/24/90
SM CT2 CT2 HA2 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 CT3 0.3100 3 0.00 ! ALLOW SUL ALI
! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90
SM SM CT2 HA2 0.1580 3 0.00 ! ALLOW ALI SUL ION
! expt. dimethyldisulfide, 3/26/92 (FL)
SM SM CT3 HA3 0.1580 3 0.00 ! ALLOW ALI SUL ION
! expt. dimethyldisulfide, 3/26/92 (FL)
SS CS CT3 HA3 0.1500 3 0.00 ! ALLOW SUL
! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
X C NC2 X 2.2500 2 180.00 ! ALLOW PEP POL ARO
! 9.0->2.25 GUANIDINIUM (KK)
X CD OH1 X 2.0500 2 180.00 ! ALLOW PEP POL ARO ALC
! adm jr, 10/17/90, acetic acid C-Oh rotation barrier
X CD OS X 2.0500 2 180.00 ! ALLOW PEP POL
! adm jr. 3/19/92, from lipid methyl acetate
X CE1 CE1 X 0.1500 1 0.00
! 2-butene, adm jr., 2/00 update
X CE1 CE1 X 8.5000 2 180.00
! 2-butene, adm jr., 2/00 update
X CE2 CE2 X 4.9000 2 180.00 !
! for ethene, yin/adm jr., 12/95
X CP1 C X 0.0000 6 180.00 ! ALLOW POL PEP PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
X CP1 CC X 0.0000 6 180.00 ! ALLOW POL PEP
! changed to 0.0 RLD 5/19/92
X CP1 CD X 0.0000 6 180.00 ! ALLOW POL PEP
! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
X CP1 CP2 X 0.1400 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
X CP2 CP2 X 0.1600 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
X CP3 CP2 X 0.1400 3 0.00 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
X 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 0.1900 3 0.00 ! ALLOW ALI
! alkane, 4/98, yin and mackerell
X CT2 CT3 X 0.1600 3 0.00 ! ALLOW ALI
! alkane, 4/98, yin and mackerell
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 0.1525 3 0.00 ! ALLOW ALI
! alkane, 4/98, yin and mackerell
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
!chi1/chi2 fitting, Zhu, 2011
!directly transferred parameters
NH1 CT1 CT1 HA1 0.2000 3 0.00 ! From X CT1 CT1 X
HB1 CT1 CT1 HA1 0.2000 3 0.00 ! From X CT1 CT1 X
HB1 CT1 CT1 CT3 0.2000 3 0.00 ! From X CT1 CT1 X
HA1 CT1 CT1 C 0.2000 3 0.00 ! From X CT1 CT1 X
!
NH1 CT1 CT2 HA2 0.2000 3 0.00 ! From X CT1 CT2 X
HB1 CT1 CT2 HA2 0.2000 3 0.00 ! From X CT1 CT2 X
HB1 CT1 CT2 OH1 0.2000 3 0.00 ! From X CT1 CT2 X
HB1 CT1 CT2 CT2 0.2000 3 0.00 ! From X CT1 CT2 X
HA2 CT2 CT1 C 0.2000 3 0.00 ! From X CT1 CT2 X
HA2 CT2 OH1 H 0.1400 3 0.00 ! From X CT2 OH1 X
!
CT1 CT2 CT2 HA2 0.1900 3 0.00 ! From X CT2 CT2 X
HA2 CT2 CT2 HA2 0.1900 3 0.00 ! From X CT2 CT2 X
HA2 CT2 CT2 CC 0.1900 3 0.00 ! From X CT2 CT2 X
!
HB1 CT1 CT2 S 0.2000 3 0.00 ! From X CT1 CT2 X
!Arg
CT2 CT2 CT2 HA2 0.1900 3 0.00 ! From X CT2 CT2 X
CT2 CT2 CT2 NC2 0.1900 3 0.00 ! From X CT2 CT2 X
CT2 CT2 NC2 HC 0.0000 6 180.00 ! From X CT2 NC2 X
CT2 CT2 NC2 C 0.0000 6 180.00 ! From X CT2 NC2 X
HA2 CT2 CT2 NC2 0.1900 3 0.00 ! From X CT2 CT2 X
CT2 NC2 C NC2 2.2500 2 180.00 ! From X C NC2 X
HA2 CT2 NC2 HC 0.0000 6 180.00 ! From X CT2 NC2 X
HA2 CT2 NC2 C 0.0000 6 180.00 ! From X CT2 NC2 X
NC2 C NC2 HC 2.2500 2 180.00 ! From X C NC2 X
!Asn
HB1 CT1 CT2 CC 0.2000 3 0.00 ! From X CT1 CT2 X
!Trp
HB1 CT1 CT2 CY 0.2000 3 0.00 ! From X CT1 CT2 X
!Asp
HA2 CT2 CC OC 0.0500 6 180.00 ! From X CT2 CC X
!Hsd/Hse
HB1 CT1 CT2 CPH1 0.2000 3 0.00 ! From X CT1 CT2 X
!Ile,Leu,Val
CT1 CT1 CT3 HA3 0.2000 3 0.00 ! From X CT1 CT3 X
CT1 CT1 CT2 HA2 0.2000 3 0.00 ! From X CT1 CT2 X
HB1 CT1 CT1 CT2 0.2000 3 0.00 ! From X CT1 CT1 X
CT1 CT2 CT3 HA3 0.1600 3 0.00 ! From X CT2 CT3 X
HA1 CT1 CT3 HA3 0.2000 3 0.00 ! From X CT1 CT3 X
HA1 CT1 CT2 HA2 0.2000 3 0.00 ! From X CT1 CT2 X
HA1 CT1 CT2 CT3 0.2000 3 0.00 ! From X CT1 CT2 X
CT3 CT1 CT2 HA2 0.2000 3 0.00 ! From X CT1 CT2 X
CT3 CT1 CT2 CT3 0.2000 3 0.00 ! From X CT1 CT2 X
HA3 CT3 CT1 CT2 0.2000 3 0.00 ! From X CT1 CT3 X
HA2 CT2 CT3 HA3 0.1600 3 0.00 ! From X CT2 CT3 X
CT1 CT2 CT1 HA1 0.2000 3 0.00 ! From X CT1 CT2 X
HB1 CT1 CT2 CT1 0.2000 3 0.00 ! From X CT1 CT2 X
CT3 CT1 CT3 HA3 0.2000 3 0.00 ! From X CT1 CT3 X
!Lys
CT2 CT2 CT2 NH3 0.1900 3 0.00 ! From X CT2 CT2 X
CT2 CT2 NH3 HC 0.1000 3 0.00 ! From X CT2 NH3 X
HA2 CT2 CT2 NH3 0.1900 3 0.00 ! From X CT2 CT2 X
HA2 CT2 NH3 HC 0.1000 3 0.00 ! From X CT2 NH3 X
!Tyr/Phe
HB1 CT1 CT2 CA 0.2000 3 0.00 ! From X CT1 CT2 X
HA2 CT2 CA CA 0.0000 6 0.00 ! From X CT2 CA X
!Thr
HB1 CT1 CT1 OH1 0.2000 3 0.00 ! From X CT1 CT1 X
HA1 CT1 OH1 H 0.1400 3 0.00 ! From X CT1 OH1 X
OH1 CT1 CT3 HA3 0.2000 3 0.00 ! From X CT1 CT3 X
!Gln
CT2 CT2 CC O 0.0500 6 180.00 ! From X CT2 CC X
CT2 CT2 CC NH2 0.0500 6 180.00 ! From X CT2 CC X
!Glu
CT2 CT2 CC OC 0.0500 6 180.00 ! From X CT2 CC X
!Glu/Hsp
NH1 CT1 CT2A HA2 0.2000 3 0.00 ! From X CT1 CT2 X
NH3 CT1 CT2A CT2 0.2000 3 0.00 ! From X CT1 CT2 X !N terminus
CT1 CT2A CT2 HA2 0.1900 3 0.00 ! From X CT2 CT2 X
HB1 CT1 CT2A HA2 0.2000 3 0.00 ! From X CT1 CT2 X
HB1 CT1 CT2A CT2 0.2000 3 0.00 ! From X CT1 CT2 X
HA2 CT2A CT1 C 0.2000 3 0.00 ! From X CT1 CT2 X
HA2 CT2A CT1 CC 0.2000 3 0.00 ! RB: added for C-ter Glu
HA2 CT2A CT2 HA2 0.1900 3 0.00 ! From X CT2 CT2 X
HA2 CT2A CT2 CC 0.1900 3 0.00 ! From X CT2 CT2 X
HB1 CT1 CT2A CPH1 0.2000 3 0.00 ! From X CT1 CT2 X
C NH1 CT1 CT2A 1.8000 1 0.00 ! from CT2 CT1 NH1 C
H NH1 CT1 CT2A 0.0000 1 0.00 ! from H NH1 CT1 CT2
CT2A CT1 C O 1.4000 1 0.00 ! from O C CT1 CT2
CT2A CT1 C NH1 0.0000 1 0.00 ! NH1 C CT1 CT2
CT2A CT1 C N 0.0000 1 0.00 ! RB: added for GLU-PRO in UBQ
! Glup
CT1 CT2A CT2 CD 0.1900 3 0.00 ! From X CT2 CT2 X
HA2 CT2A CT2 CD 0.1900 3 0.00 ! From X CT2 CT2 X
CT2A CPH1 CPH1 HR1 1.0000 2 180.00 ! from HR1 CPH1 CPH1 CT2
CT2A CPH1 CPH1 NR3 2.5000 2 180.00 ! from NR3 CPH1 CPH1 CT2
CT2A CPH1 NR3 H 3.0000 2 180.00 ! from H NR3 CPH1 CT2
CT2A CPH1 NR3 CPH2 2.5000 2 180.00 ! from CT2 CPH1 NR3 CPH2
HA2 CT2A CPH1 CPH1 0.0000 3 0.00 ! from HA2 CT2 CPH1 CPH1
HA2 CT2A CPH1 NR3 0.1900 3 0.00 ! from NR3 CPH1 CT2 HA2
! Fit dihedrals
! Variable cutoff based on QM and weighted in favor of alphaR and EXT (5:5:1)
! Shared dihedrals were fitted simultaneously
! Group-fitted for Lys/Arg/Gln/Met
C CT1 CT2 CT2 0.3500 1 180.00
C CT1 CT2 CT2 0.4200 2 180.00
C CT1 CT2 CT2 1.9100 3 180.00
CT2 CT2 CT1 NH1 0.8800 1 180.00
CT2 CT2 CT1 NH1 0.0000 2 180.00
CT2 CT2 CT1 NH1 1.9000 3 0.00
CC CT2 CT2 CT1 1.8400 1 180.00
CC CT2 CT2 CT1 0.8400 2 180.00
CC CT2 CT2 CT1 0.3900 3 180.00
CT1 CT2 CT2 CT2 0.6300 1 180.00
CT1 CT2 CT2 CT2 0.0100 2 0.00
CT1 CT2 CT2 CT2 0.1500 3 0.00
CT1 CT2 CT2 S 0.1400 1 180.00
CT1 CT2 CT2 S 0.5400 2 0.00
CT1 CT2 CT2 S 0.6900 3 0.00
! Fitted Asn
C CT1 CT2 CC 1.4100 1 180.00
C CT1 CT2 CC 1.2900 2 180.00
C CT1 CT2 CC 0.5900 3 180.00
CC CT2 CT1 NH1 0.2800 1 180.00
CC CT2 CT1 NH1 0.5000 2 180.00
CC CT2 CT1 NH1 0.3800 3 0.00
CT1 CT2 CC NH2 0.6200 1 180.00
CT1 CT2 CC NH2 0.6600 2 180.00
CT1 CT2 CC NH2 0.7200 3 180.00
CT1 CT2 CC O 0.4200 1 180.00
CT1 CT2 CC O 0.1500 2 180.00
CT1 CT2 CC O 0.9500 3 180.00
! Fitted Asp
C CT1 CT2A CC 1.6100 1 180.00
C CT1 CT2A CC 1.2900 2 180.00
C CT1 CT2A CC 0.5900 3 180.00
CC CT2A CT1 NH1 0.6800 1 180.00
CC CT2A CT1 NH1 0.1000 2 180.00
CC CT2A CT1 NH1 0.3800 3 0.00
CT1 CT2A CC OC 0.8400 1 0.00
CT1 CT2A CC OC 0.9800 2 180.00
CT1 CT2A CC OC 1.4600 3 0.00
! Fitted Cys
CT1 CT2 S HS 0.2000 1 0.00
CT1 CT2 S HS 0.6500 2 0.00
CT1 CT2 S HS 0.2200 3 0.00
C CT1 CT2 S 0.2400 1 180.00
C CT1 CT2 S 0.7500 2 180.00
C CT1 CT2 S 1.3500 3 180.00
NH1 CT1 CT2 S 0.3400 1 0.00
NH1 CT1 CT2 S 0.5000 2 180.00
NH1 CT1 CT2 S 1.4300 3 0.00
! Fitted Glu
CC CT2 CT2A CT1 0.0000 1 180.00
CC CT2 CT2A CT1 0.3800 2 180.00
CC CT2 CT2A CT1 0.5900 3 180.00
C CT1 CT2A CT2 0.1100 1 0.00
C CT1 CT2A CT2 0.9800 2 180.00
C CT1 CT2A CT2 1.6000 3 180.00
CC CT1 CT2A CT2 1.6000 3 180.00
CT2 CT2A CT1 NH1 0.3000 1 0.00
CT2 CT2A CT1 NH1 0.3500 2 0.00
CT2 CT2A CT1 NH1 1.7600 3 0.00
! Group-fitted for Hsd/Hse
CPH1 CPH1 CT2 CT1 1.7400 1 0.00
CPH1 CPH1 CT2 CT1 0.1500 2 0.00
CPH1 CPH1 CT2 CT1 0.7700 3 180.00
CT1 CT2 CPH1 NR1 1.4900 1 0.00
CT1 CT2 CPH1 NR1 0.0900 2 180.00
CT1 CT2 CPH1 NR1 0.7900 3 180.00
CT1 CT2 CPH1 NR2 1.0900 1 0.00
CT1 CT2 CPH1 NR2 0.0900 2 0.00
CT1 CT2 CPH1 NR2 0.6700 3 180.00
C CT1 CT2 CPH1 0.1800 1 180.00
C CT1 CT2 CPH1 0.6400 2 180.00
C CT1 CT2 CPH1 0.8700 3 180.00
CPH1 CT2 CT1 NH1 0.0000 1 0.00
CPH1 CT2 CT1 NH1 0.0000 2 180.00
CPH1 CT2 CT1 NH1 0.9000 3 0.00
! Fitted Hsp
CPH1 CPH1 CT2A CT1 2.0400 1 0.00
CPH1 CPH1 CT2A CT1 0.4400 2 0.00
CPH1 CPH1 CT2A CT1 0.1300 3 180.00
CT1 CT2A CPH1 NR3 0.5300 1 180.00
CT1 CT2A CPH1 NR3 0.4200 2 180.00
CT1 CT2A CPH1 NR3 0.3000 3 180.00
C CT1 CT2A CPH1 1.7500 1 180.00
C CT1 CT2A CPH1 0.1300 2 0.00
C CT1 CT2A CPH1 1.8600 3 180.00
CPH1 CT2A CT1 NH1 1.0900 1 180.00
CPH1 CT2A CT1 NH1 0.2200 2 180.00
CPH1 CT2A CT1 NH1 2.3200 3 0.00
! Group-fitted for Ile/Thr
CT1 CT1 CT2 CT3 0.3800 1 180.00
CT1 CT1 CT2 CT3 0.1300 2 180.00
CT1 CT1 CT2 CT3 0.2900 3 180.00
C CT1 CT1 CT2 0.1000 1 180.00
C CT1 CT1 CT2 0.5200 2 180.00
C CT1 CT1 CT2 0.2900 3 180.00
CT2 CT1 CT1 NH1 0.1200 1 180.00
CT2 CT1 CT1 NH1 0.3600 2 180.00
CT2 CT1 CT1 NH1 0.4100 3 0.00
! Fitted Leu
CT1 CT2 CT1 CT3 0.0500 1 0.00
CT1 CT2 CT1 CT3 0.1000 2 180.00
CT1 CT2 CT1 CT3 0.0100 3 180.00
C CT1 CT2 CT1 0.3200 1 180.00
C CT1 CT2 CT1 0.6100 2 180.00
C CT1 CT2 CT1 0.7200 3 180.00
CT1 CT2 CT1 NH1 0.4800 1 180.00
CT1 CT2 CT1 NH1 0.4200 2 180.00
CT1 CT2 CT1 NH1 0.6500 3 0.00
! Group-fitted for Phe/Tyr
CA CA CT2 CT1 1.0700 1 0.00
CA CA CT2 CT1 0.2400 2 180.00
CA CA CT2 CT1 0.1700 3 180.00
C CT1 CT2 CA 1.2800 1 180.00
C CT1 CT2 CA 0.9400 2 180.00
C CT1 CT2 CA 1.5700 3 180.00
CA CT2 CT1 NH1 0.5200 1 180.00
CA CT2 CT1 NH1 0.6200 2 180.00
CA CT2 CT1 NH1 1.5800 3 0.00
! Fitted Ser
CT1 CT2 OH1 H 0.0200 1 0.00
CT1 CT2 OH1 H 0.5600 2 0.00
CT1 CT2 OH1 H 0.4900 3 0.00
C CT1 CT2 OH1 0.6500 1 180.00
C CT1 CT2 OH1 0.2500 2 180.00
C CT1 CT2 OH1 1.1700 3 180.00
NH1 CT1 CT2 OH1 0.1800 1 180.00
NH1 CT1 CT2 OH1 0.1900 2 180.00
NH1 CT1 CT2 OH1 1.4600 3 0.00
! Group-fitted for Ile/Thr
CT1 CT1 OH1 H 0.1800 1 0.00
CT1 CT1 OH1 H 0.0600 2 0.00
CT1 CT1 OH1 H 0.2500 3 0.00
C CT1 CT1 OH1 0.7900 1 180.00
C CT1 CT1 OH1 0.3900 2 180.00
C CT1 CT1 OH1 0.9900 3 180.00
NH1 CT1 CT1 OH1 0.0900 1 0.00
NH1 CT1 CT1 OH1 0.1900 2 180.00
NH1 CT1 CT1 OH1 0.1700 3 0.00
! Fitted Trp
CA CY CT2 CT1 0.0300 1 0.00
CA CY CT2 CT1 0.5500 2 0.00
CA CY CT2 CT1 0.3900 3 180.00
CPT CY CT2 CT1 0.3600 1 180.00
CPT CY CT2 CT1 0.0500 2 0.00
CPT CY CT2 CT1 0.1900 3 180.00
C CT1 CT2 CY 1.0900 1 180.00
C CT1 CT2 CY 0.5000 2 180.00
C CT1 CT2 CY 1.1700 3 180.00
CY CT2 CT1 NH1 0.2900 1 180.00
CY CT2 CT1 NH1 0.6600 2 180.00
CY CT2 CT1 NH1 1.1700 3 0.00
! Fitted Val
C CT1 CT1 CT3 0.1400 1 180.00
C CT1 CT1 CT3 0.2600 2 180.00
C CT1 CT1 CT3 0.3300 3 180.00
CT3 CT1 CT1 NH1 0.1800 1 0.00
CT3 CT1 CT1 NH1 0.0600 2 0.00
CT3 CT1 CT1 NH1 0.5900 3 0.00
!ASP, CT2->CT2A, jshim
H NH1 CT2A CC 0.0000 1 0.00
X CT2A CC X 0.0500 6 180.00
HB1 CT1 CT2A CC 0.2000 3 0.00
HA2 CT2A CC OC 0.0500 6 180.00
NH3 CT1 CT2A HA2 0.2000 3 0.00
NH3 CT1 CT2A CC 0.2000 3 0.00
CC CT2A CT1 CC 0.2000 3 0.00
!termini specific terms
CPH1 CT2A CT1 CC 0.2000 3 0.00
CPH1 CT2A CT1 NH3 0.2000 3 0.00
HA2 CT2A CT1 CD 0.2000 3 0.00
CPH1 CT2A CT1 CD 0.2000 3 0.00
CT2 CT2A CT1 CD 0.2000 3 0.00
CC CT2A CT1 CD 0.2000 3 0.00
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
!
HE2 HE2 CE2 CE2 3.0 0 0.00 !
! for ethene, yin/adm jr., 12/95
HR1 NR1 NR2 CPH2 0.5000 0 0.0000 ! ALLOW ARO
! his, adm jr., 7/05/90
HR1 NR2 NR1 CPH2 0.5000 0 0.0000 ! ALLOW ARO
! his, adm jr., 7/05/90
HR3 CPH1 NR1 CPH1 0.5000 0 0.0000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HR3 CPH1 NR2 CPH1 0.5000 0 0.0000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HR3 CPH1 NR3 CPH1 1.0000 0 0.0000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HR3 NR1 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HR3 NR2 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
N C CP1 CP3 0.0000 0 0.0000 ! ALLOW PRO
! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92
NC2 X X C 45.0000 0 0.0000 ! ALLOW PEP POL ARO
! mp2/6-311g** guan vibrational data, adm jr., 1/04
C HC HC NC2 0.0 0 0.0
! mp2/6-311g** guan vibrational data, adm jr., 1/04
NC2 X X HC -2.0 0 0.0
! mp2/6-311g** guan vibrational data, adm jr., 1/04
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
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
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 HA1 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 HA1 CC 45.0000 0 0.0000 ! ALLOW PEP POL
! adm jr., 5/13/91, formamide geometry and vibrations
O X X C 120.0000 0 0.0000 ! ALLOW PEP POL ARO
! NMA Vibrational Modes (LK)
OB X X CD 100.0000 0 0.0000 ! ALLOW ALC ARO POL
! adm jr., 10/17/90, acetic acid vibrations
OC X X CC 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
! 90.0->96.0 acetate, single impr (KK)
CC X X CT1 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
! 90.0->96.0 acetate, single impr (KK)
CC X X CT2 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
! 90.0->96.0 acetate, single impr (KK)
CC X X CT3 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
! 90.0->96.0 acetate, single impr (KK)
CMAP
! 2D grid correction data.
! Finalfix3, Feig/Best/MacKerell 2010
! alanine map
C NH1 CT1 C NH1 CT1 C NH1 24
! phi = -180.0
0.126790 0.768700 0.971260 1.250970 2.121010
2.720430 2.089440 1.789790 0.780870 -0.688474
1.001130 -2.200520 -4.827670 -4.821447 -4.913223
-3.591106 -2.766446 -2.784200 -2.454589 -2.346991
-2.335350 -1.522656 -0.951542 -0.036650
! phi = -165.0
-0.127133 1.377090 1.577020 1.872290 2.398990
2.486630 2.436754 1.929070 1.086456 0.643400
0.258676 -2.800440 -4.009477 -4.135306 -3.420090
-2.602140 -2.299128 -1.501241 -1.101780 -0.861434
-0.640168 -0.207701 -1.076344 -1.122030
! phi = -150.0
0.084069 1.420317 1.624350 2.047200 2.653910
2.716410 2.321416 1.985454 1.557466 2.463293
-0.225720 -1.815886 -2.583256 -3.006154 -2.551995
-1.890683 -1.354215 -0.727243 0.068512 -0.225016
-0.765479 -1.283444 -1.293226 -0.816303
! phi = -135.0
0.927992 1.521370 2.242218 2.546305 3.111384
2.918410 2.460813 2.187970 2.058314 1.852278
0.115935 -1.183897 -1.995479 -2.278329 -1.959136
-1.340467 -0.932949 0.021790 0.313725 -0.517358
-1.152891 -0.983285 -0.566518 -0.442565
! phi = -120.0
1.357468 1.959160 2.698894 3.037857 3.698960
3.558453 2.639296 2.773853 2.719664 1.627997
0.705667 -0.785637 -2.118268 -2.628489 -1.803113
-0.425969 -0.062320 0.439040 0.910952 -0.546994
-0.968118 -0.856791 -0.250116 0.449309
! phi = -105.0
2.045006 2.544424 2.818030 3.088582 3.370620
3.551568 3.073520 2.903794 2.956634 2.124759
0.906487 -0.823628 -2.090819 -2.241579 -1.456524
0.206160 0.082195 0.771710 1.040241 -0.124647
-0.316550 -0.164333 0.314474 0.733747
! phi = -90.0
1.451735 2.748481 2.738185 3.156796 3.450028
3.344157 3.180200 3.898724 3.335030 2.440579
0.912671 -0.606502 -1.511772 -1.620864 -0.962798
-0.020653 0.415153 0.908250 0.459433 0.145910
-0.071054 0.017622 0.280839 0.748823
! phi = -75.0
1.378160 3.345958 2.352424 3.063543 3.814070
3.700796 3.580310 4.212293 3.536425 1.693809
0.095172 -0.682452 -0.123614 -0.427765 -0.598368
0.226352 0.423308 0.301999 0.551890 0.191719
-0.253585 -0.190548 -0.253412 0.468922
! phi = -60.0
0.237754 1.229980 1.716960 3.168570 4.208190
4.391860 4.276080 3.673107 2.272295 -0.482789
-0.406695 -0.038919 -0.357600 -0.823341 -0.173146
0.139806 0.267796 0.322420 0.309664 -0.666399
-0.948631 -1.534365 -1.479968 -0.204264
! phi = -45.0
-1.184837 0.078060 2.347410 4.211350 5.376000
5.389940 4.380200 2.461506 1.123713 0.107016
0.007574 -0.149443 -0.797230 -0.582210 0.082910
0.271580 -0.045570 0.379430 0.247770 -0.890956
-1.582430 -1.954532 -1.980965 -2.000433
! phi = -30.0
-1.174720 1.067030 4.180460 6.741610 6.070770
4.806470 2.783340 1.320806 0.765978 -0.008448
0.276860 -0.707140 1.314360 1.522590 1.915550
2.223490 0.194290 0.534000 0.331780 -1.595147
-2.849141 -3.550465 -3.277369 -2.655135
! phi = -15.0
0.293590 5.588070 3.732620 3.217620 3.272450
2.517320 1.588700 1.381760 0.856410 0.655170
1.616970 0.846920 0.511070 0.740760 1.021020
1.616580 -0.342400 0.181770 -0.613920 -2.558037
-3.786839 -3.807325 -3.155346 -1.749204
! phi = 0.0
2.832310 0.787990 0.323280 0.479230 0.628600
0.976330 1.238750 1.671950 1.645480 2.520340
1.606970 0.776350 0.119780 0.070390 0.121170
-1.569230 -1.213010 -1.846360 -2.744510 -3.792530
-3.934880 -3.615930 -2.675750 -0.924170
! phi = 15.0
-0.778340 -1.912680 -2.052140 -1.846280 -1.047430
0.183400 1.682950 2.223500 1.358370 2.448660
1.436920 0.678570 -0.237060 -0.535320 -0.790380
-2.182580 -3.251140 -4.195110 -4.269270 -3.908210
-3.455620 -2.773970 1.755370 0.313410
! phi = 30.0
-2.963810 -3.483730 -3.441809 -2.400349 -1.125083
0.336200 1.428450 1.394630 0.970370 2.462720
1.522430 0.553620 -0.407380 -1.482950 -3.613920
-4.159810 -4.709721 -4.496271 -3.764540 -2.959140
-1.963850 -1.071260 -1.599580 -2.445320
! phi = 45.0
-4.021496 -3.836549 -3.365327 -2.334377 -0.984725
0.362000 0.814380 0.754110 0.502370 1.903420
0.770220 -0.416420 -3.286310 -3.875270 -4.611550
-5.287977 -5.146239 -4.038627 -2.865450 -2.368170
-2.860490 -3.416560 -3.666490 -3.595217
! phi = 60.0
-3.353683 -2.984416 -2.317412 -1.240143 -0.257890
0.722610 0.668070 0.438130 2.395330 1.632470
-2.041450 -3.218100 -3.915080 -4.568574 -5.096776
-5.526955 -5.005312 -3.777879 -2.840678 -3.508820
-3.756430 -3.640810 -3.451845 -3.342810
! phi = 75.0
-2.248733 -1.641080 -1.010583 0.039656 0.636063
0.823710 0.517140 -0.013120 -0.370910 -1.192809
-2.305650 -3.420580 -4.484960 -5.597237 -5.601264
-5.727739 -4.740525 -3.819378 -3.685150 -4.151360
-4.170739 -3.725589 -3.736732 -2.620673
! phi = 90.0
-1.720840 -1.177830 -0.428430 0.277730 0.807900
0.803260 0.482510 -0.336900 -0.786270 -1.774070
-2.793220 -3.828560 -5.211800 -6.294328 -6.617221
-5.763953 -5.072995 -3.911450 -4.158306 -4.473413
-4.099325 -3.769822 -3.157300 -2.651694
! phi = 105.0
-1.850640 -1.092420 -0.445020 0.128490 1.005520
0.884820 0.485850 -0.218470 -0.857670 -1.682330
-3.014400 -4.481110 -6.053510 -6.865400 -6.871130
-5.728240 -3.912230 -4.802110 -5.034640 -4.715990
-4.600554 -4.086721 -3.274630 -2.410940
! phi = 120.0
-1.969230 -1.116650 -0.540250 -0.150330 0.763520
1.038890 0.758480 0.313530 -0.333050 -1.872770
-3.366270 -5.008260 -6.124810 -7.034830 -6.724320
-3.700200 -4.510620 -5.185650 -5.361620 -4.847490
-4.444320 -4.004260 -3.415720 -2.751230
! phi = 135.0
-2.111250 -1.168960 -0.322790 -0.006920 0.316660
1.086270 0.939170 0.625340 -0.166360 -1.830310
-3.469470 -4.946030 -6.112560 -1.915580 -4.047310
-4.996740 -4.996730 -4.842690 -4.886620 -4.300540
-4.494620 -4.442210 -4.163570 -3.183510
! phi = 150.0
-1.757590 -0.403620 0.023920 0.362390 0.634520
1.264920 1.361360 0.948420 -0.073680 -1.483560
-3.152820 1.835120 -1.762860 -5.093660 -5.744830
-5.390070 -4.783930 -4.190630 -4.115420 -4.042280
-4.125570 -4.028550 -4.026100 -2.937910
! phi = 165.0
-0.810590 -0.071500 0.378890 0.543310 1.277880
1.641310 1.698840 1.519950 0.631950 -1.088670
-2.736530 -0.735240 -4.563830 -6.408350 -5.889450
-5.141750 -4.194970 -3.666490 -3.843450 -3.555000
-3.548722 -3.246995 -2.751289 -1.814368
! alanine before proline map
C NH1 CT1 C NH1 CT1 C N 24
! phi = -180.0
0.126790 0.768700 0.971260 1.250970 2.121010
2.720430 2.089440 1.789790 0.780870 -0.688474
1.001130 -2.200520 -4.827670 -4.821447 -4.913223
-3.591106 -2.766446 -2.784200 -2.454589 -2.346991
-2.335350 -1.522656 -0.951542 -0.036650
! phi = -165.0
-0.127133 1.377090 1.577020 1.872290 2.398990
2.486630 2.436754 1.929070 1.086456 0.643400
0.258676 -2.800440 -4.009477 -4.135306 -3.420090
-2.602140 -2.299128 -1.501241 -1.101780 -0.861434
-0.640168 -0.207701 -1.076344 -1.122030
! phi = -150.0
0.084069 1.420317 1.624350 2.047200 2.653910
2.716410 2.321416 1.985454 1.557466 2.463293
-0.225720 -1.815886 -2.583256 -3.006154 -2.551995
-1.890683 -1.354215 -0.727243 0.068512 -0.225016
-0.765479 -1.283444 -1.293226 -0.816303
! phi = -135.0
0.927992 1.521370 2.242218 2.546305 3.111384
2.918410 2.460813 2.187970 2.058314 1.852278
0.115935 -1.183897 -1.995479 -2.278329 -1.959136
-1.340467 -0.932949 0.021790 0.313725 -0.517358
-1.152891 -0.983285 -0.566518 -0.442565
! phi = -120.0
1.357468 1.959160 2.698894 3.037857 3.698960
3.558453 2.639296 2.773853 2.719664 1.627997
0.705667 -0.785637 -2.118268 -2.628489 -1.803113
-0.425969 -0.062320 0.439040 0.910952 -0.546994
-0.968118 -0.856791 -0.250116 0.449309
! phi = -105.0
2.045006 2.544424 2.818030 3.088582 3.370620
3.551568 3.073520 2.903794 2.956634 2.124759
0.906487 -0.823628 -2.090819 -2.241579 -1.456524
0.206160 0.082195 0.771710 1.040241 -0.124647
-0.316550 -0.164333 0.314474 0.733747
! phi = -90.0
1.451735 2.748481 2.738185 3.156796 3.450028
3.344157 3.180200 3.898724 3.335030 2.440579
0.912671 -0.606502 -1.511772 -1.620864 -0.962798
-0.020653 0.415153 0.908250 0.459433 0.145910
-0.071054 0.017622 0.280839 0.748823
! phi = -75.0
1.378160 3.345958 2.352424 3.063543 3.814070
3.700796 3.580310 4.212293 3.536425 1.693809
0.095172 -0.682452 -0.123614 -0.427765 -0.598368
0.226352 0.423308 0.301999 0.551890 0.191719
-0.253585 -0.190548 -0.253412 0.468922
! phi = -60.0
0.237754 1.229980 1.716960 3.168570 4.208190
4.391860 4.276080 3.673107 2.272295 -0.482789
-0.406695 -0.038919 -0.357600 -0.823341 -0.173146
0.139806 0.267796 0.322420 0.309664 -0.666399
-0.948631 -1.534365 -1.479968 -0.204264
! phi = -45.0
-1.184837 0.078060 2.347410 4.211350 5.376000
5.389940 4.380200 2.461506 1.123713 0.107016
0.007574 -0.149443 -0.797230 -0.582210 0.082910
0.271580 -0.045570 0.379430 0.247770 -0.890956
-1.582430 -1.954532 -1.980965 -2.000433
! phi = -30.0
-1.174720 1.067030 4.180460 6.741610 6.070770
4.806470 2.783340 1.320806 0.765978 -0.008448
0.276860 -0.707140 1.314360 1.522590 1.915550
2.223490 0.194290 0.534000 0.331780 -1.595147
-2.849141 -3.550465 -3.277369 -2.655135
! phi = -15.0
0.293590 5.588070 3.732620 3.217620 3.272450
2.517320 1.588700 1.381760 0.856410 0.655170
1.616970 0.846920 0.511070 0.740760 1.021020
1.616580 -0.342400 0.181770 -0.613920 -2.558037
-3.786839 -3.807325 -3.155346 -1.749204
! phi = 0.0
2.832310 0.787990 0.323280 0.479230 0.628600
0.976330 1.238750 1.671950 1.645480 2.520340
1.606970 0.776350 0.119780 0.070390 0.121170
-1.569230 -1.213010 -1.846360 -2.744510 -3.792530
-3.934880 -3.615930 -2.675750 -0.924170
! phi = 15.0
-0.778340 -1.912680 -2.052140 -1.846280 -1.047430
0.183400 1.682950 2.223500 1.358370 2.448660
1.436920 0.678570 -0.237060 -0.535320 -0.790380
-2.182580 -3.251140 -4.195110 -4.269270 -3.908210
-3.455620 -2.773970 1.755370 0.313410
! phi = 30.0
-2.963810 -3.483730 -3.441809 -2.400349 -1.125083
0.336200 1.428450 1.394630 0.970370 2.462720
1.522430 0.553620 -0.407380 -1.482950 -3.613920
-4.159810 -4.709721 -4.496271 -3.764540 -2.959140
-1.963850 -1.071260 -1.599580 -2.445320
! phi = 45.0
-4.021496 -3.836549 -3.365327 -2.334377 -0.984725
0.362000 0.814380 0.754110 0.502370 1.903420
0.770220 -0.416420 -3.286310 -3.875270 -4.611550
-5.287977 -5.146239 -4.038627 -2.865450 -2.368170
-2.860490 -3.416560 -3.666490 -3.595217
! phi = 60.0
-3.353683 -2.984416 -2.317412 -1.240143 -0.257890
0.722610 0.668070 0.438130 2.395330 1.632470
-2.041450 -3.218100 -3.915080 -4.568574 -5.096776
-5.526955 -5.005312 -3.777879 -2.840678 -3.508820
-3.756430 -3.640810 -3.451845 -3.342810
! phi = 75.0
-2.248733 -1.641080 -1.010583 0.039656 0.636063
0.823710 0.517140 -0.013120 -0.370910 -1.192809
-2.305650 -3.420580 -4.484960 -5.597237 -5.601264
-5.727739 -4.740525 -3.819378 -3.685150 -4.151360
-4.170739 -3.725589 -3.736732 -2.620673
! phi = 90.0
-1.720840 -1.177830 -0.428430 0.277730 0.807900
0.803260 0.482510 -0.336900 -0.786270 -1.774070
-2.793220 -3.828560 -5.211800 -6.294328 -6.617221
-5.763953 -5.072995 -3.911450 -4.158306 -4.473413
-4.099325 -3.769822 -3.157300 -2.651694
! phi = 105.0
-1.850640 -1.092420 -0.445020 0.128490 1.005520
0.884820 0.485850 -0.218470 -0.857670 -1.682330
-3.014400 -4.481110 -6.053510 -6.865400 -6.871130
-5.728240 -3.912230 -4.802110 -5.034640 -4.715990
-4.600554 -4.086721 -3.274630 -2.410940
! phi = 120.0
-1.969230 -1.116650 -0.540250 -0.150330 0.763520
1.038890 0.758480 0.313530 -0.333050 -1.872770
-3.366270 -5.008260 -6.124810 -7.034830 -6.724320
-3.700200 -4.510620 -5.185650 -5.361620 -4.847490
-4.444320 -4.004260 -3.415720 -2.751230
! phi = 135.0
-2.111250 -1.168960 -0.322790 -0.006920 0.316660
1.086270 0.939170 0.625340 -0.166360 -1.830310
-3.469470 -4.946030 -6.112560 -1.915580 -4.047310
-4.996740 -4.996730 -4.842690 -4.886620 -4.300540
-4.494620 -4.442210 -4.163570 -3.183510
! phi = 150.0
-1.757590 -0.403620 0.023920 0.362390 0.634520
1.264920 1.361360 0.948420 -0.073680 -1.483560
-3.152820 1.835120 -1.762860 -5.093660 -5.744830
-5.390070 -4.783930 -4.190630 -4.115420 -4.042280
-4.125570 -4.028550 -4.026100 -2.937910
! phi = 165.0
-0.810590 -0.071500 0.378890 0.543310 1.277880
1.641310 1.698840 1.519950 0.631950 -1.088670
-2.736530 -0.735240 -4.563830 -6.408350 -5.889450
-5.141750 -4.194970 -3.666490 -3.843450 -3.555000
-3.548722 -3.246995 -2.751289 -1.814368
! proline
! mp2/aug-cc-pVDZ//RIMP2/VTZ/VQZ CBS map
C N CP1 C N CP1 C NH1 24
! phi = -180
2.973500 3.348200 3.062900 2.113400 1.040500
0.770600 0.785200 0.263300 -0.479000 -0.583000
-0.463800 -0.292600 0.000000 0.259100 0.177100
-0.151200 -0.173500 0.211700 0.348900 -0.135600
-0.950000 -1.256600 -0.292800 1.560000
! phi = -165
5.674100 6.011400 5.562700 4.467300 3.390800
3.008800 2.848600 2.311200 1.661400 1.468400
1.142700 1.437400 2.113200 2.799500 2.989100
2.869000 3.016100 3.328500 3.232900 2.547600
1.647200 1.422700 2.517100 4.339800
! phi = -150
6.752800 6.973200 6.444300 5.389800 4.438600
4.046000 3.832800 3.442400 3.303500 3.010000
2.838100 3.162200 3.778300 4.362800 4.603600
4.546200 4.702100 4.837200 4.549500 3.849600
3.099200 3.031800 4.060200 5.624800
! phi = -135
7.627800 8.153400 7.342500 5.893500 4.799200
4.433400 4.551500 4.442800 2.222200 0.776300
0.790000 2.152300 3.932900 5.274900 5.830800
5.988600 5.588500 5.211000 4.918000 4.292100
3.495500 3.449800 4.617700 6.311700
! phi = -120
8.115600 8.477200 7.754300 6.585000 5.537900
4.964300 4.929000 4.421200 2.336100 1.257800
1.769300 3.359900 5.018000 6.055500 6.217600
5.726100 5.512200 5.820200 5.716700 4.872300
4.066800 4.094600 5.284900 6.931500
! phi = -105
9.249700 9.483000 8.668500 7.525300 7.003200
6.834600 6.822100 5.287600 3.320600 2.640300
3.464800 5.100300 6.537600 6.885600 5.842000
5.248700 5.540200 6.652400 7.196700 6.625400
5.710100 5.581700 6.651500 8.192800
! phi = -90
9.335600 9.208000 8.564600 8.010200 7.885100
8.212200 8.737100 8.429100 7.306500 6.474200
6.651300 7.484700 8.195300 8.295000 7.407200
6.529900 6.242000 6.227500 6.347300 6.449700
6.404700 6.579300 7.391700 8.570700
! phi = -75
10.955200 11.455400 11.173300 10.428700 10.062400
10.044500 9.279600 6.965100 5.361500 5.102700
6.267600 7.871600 8.009800 7.104500 6.616400
6.733700 7.504000 8.664700 9.282800 8.795900
7.872500 7.612400 8.498100 9.894000
! phi = -60
8.422900 8.529200 8.608500 9.306400 10.239400
11.025900 11.510800 9.283500 7.566000 6.624600
7.038700 8.222400 8.786400 8.512000 8.103500
7.988200 8.192900 8.291000 8.055600 7.436800
6.651800 6.317000 6.802500 7.746300
! phi = -45
6.913200 7.937400 8.610800 9.316600 9.388500
9.408400 8.828800 7.297900 5.456400 4.742700
5.793100 7.118800 7.565400 7.598500 7.438700
7.512500 7.878100 8.082200 7.642700 6.320500
4.680400 3.830500 4.215800 5.435200
! phi = -30
5.466700 7.116000 8.908800 8.347200 7.413500
7.047000 6.031600 4.193100 2.674800 3.023700
4.485300 5.451700 6.214900 6.422600 6.229300
6.191100 6.488900 6.646400 5.833400 3.751300
1.719800 1.064900 1.955800 3.860800
! phi = -15
3.061500 5.603800 12.179500 6.295200 5.323400
4.826500 3.705600 2.461500 2.291600 3.145900
3.562100 4.443600 5.337500 5.728800 5.694800
5.641600 5.943300 6.169000 4.759500 2.569400
1.357100 1.669800 3.212300 5.031900
! phi = 0
8.085900 8.051100 5.023600 3.450800 2.836100
2.192500 1.566200 1.456300 2.039300 1.945200
2.188400 2.921300 3.467500 3.543500 3.374500
3.472300 4.069900 3.615600 2.082200 0.958600
0.792600 1.494200 2.794900 4.853100
! phi = 15
6.639500 5.177400 3.252300 1.952700 1.078400
0.888300 1.505400 2.442300 2.178600 1.578600
1.777400 2.395400 2.820200 2.795200 2.662400
2.917100 2.562100 1.557900 1.322300 1.631400
2.051200 2.555600 3.039100 4.915000
! phi = 30
7.548800 5.095500 2.747000 0.955200 0.444500
1.318700 2.733300 3.223200 2.565500 2.150900
2.394400 2.939300 3.266000 3.210000 3.113400
2.491300 0.978300 0.815300 1.522700 2.055600
2.199900 2.327600 3.474200 7.977800
! phi = 45
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
! phi = 60
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
! phi = 75
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
! phi = 90
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
! phi = 105
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
! phi = 120
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
! phi = 135
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
! phi = 150
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
! phi = 165
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
!2 adjacent prolines
! mp2/aug-cc-pVDZ//RIMP2/VTZ/VQZ CBS map
C N CP1 C N CP1 C N 24
! phi = -180
2.973500 3.348200 3.062900 2.113400 1.040500
0.770600 0.785200 0.263300 -0.479000 -0.583000
-0.463800 -0.292600 0.000000 0.259100 0.177100
-0.151200 -0.173500 0.211700 0.348900 -0.135600
-0.950000 -1.256600 -0.292800 1.560000
! phi = -165
5.674100 6.011400 5.562700 4.467300 3.390800
3.008800 2.848600 2.311200 1.661400 1.468400
1.142700 1.437400 2.113200 2.799500 2.989100
2.869000 3.016100 3.328500 3.232900 2.547600
1.647200 1.422700 2.517100 4.339800
! phi = -150
6.752800 6.973200 6.444300 5.389800 4.438600
4.046000 3.832800 3.442400 3.303500 3.010000
2.838100 3.162200 3.778300 4.362800 4.603600
4.546200 4.702100 4.837200 4.549500 3.849600
3.099200 3.031800 4.060200 5.624800
! phi = -135
7.627800 8.153400 7.342500 5.893500 4.799200
4.433400 4.551500 4.442800 2.222200 0.776300
0.790000 2.152300 3.932900 5.274900 5.830800
5.988600 5.588500 5.211000 4.918000 4.292100
3.495500 3.449800 4.617700 6.311700
! phi = -120
8.115600 8.477200 7.754300 6.585000 5.537900
4.964300 4.929000 4.421200 2.336100 1.257800
1.769300 3.359900 5.018000 6.055500 6.217600
5.726100 5.512200 5.820200 5.716700 4.872300
4.066800 4.094600 5.284900 6.931500
! phi = -105
9.249700 9.483000 8.668500 7.525300 7.003200
6.834600 6.822100 5.287600 3.320600 2.640300
3.464800 5.100300 6.537600 6.885600 5.842000
5.248700 5.540200 6.652400 7.196700 6.625400
5.710100 5.581700 6.651500 8.192800
! phi = -90
9.335600 9.208000 8.564600 8.010200 7.885100
8.212200 8.737100 8.429100 7.306500 6.474200
6.651300 7.484700 8.195300 8.295000 7.407200
6.529900 6.242000 6.227500 6.347300 6.449700
6.404700 6.579300 7.391700 8.570700
! phi = -75
10.955200 11.455400 11.173300 10.428700 10.062400
10.044500 9.279600 6.965100 5.361500 5.102700
6.267600 7.871600 8.009800 7.104500 6.616400
6.733700 7.504000 8.664700 9.282800 8.795900
7.872500 7.612400 8.498100 9.894000
! phi = -60
8.422900 8.529200 8.608500 9.306400 10.239400
11.025900 11.510800 9.283500 7.566000 6.624600
7.038700 8.222400 8.786400 8.512000 8.103500
7.988200 8.192900 8.291000 8.055600 7.436800
6.651800 6.317000 6.802500 7.746300
! phi = -45
6.913200 7.937400 8.610800 9.316600 9.388500
9.408400 8.828800 7.297900 5.456400 4.742700
5.793100 7.118800 7.565400 7.598500 7.438700
7.512500 7.878100 8.082200 7.642700 6.320500
4.680400 3.830500 4.215800 5.435200
! phi = -30
5.466700 7.116000 8.908800 8.347200 7.413500
7.047000 6.031600 4.193100 2.674800 3.023700
4.485300 5.451700 6.214900 6.422600 6.229300
6.191100 6.488900 6.646400 5.833400 3.751300
1.719800 1.064900 1.955800 3.860800
! phi = -15
3.061500 5.603800 12.179500 6.295200 5.323400
4.826500 3.705600 2.461500 2.291600 3.145900
3.562100 4.443600 5.337500 5.728800 5.694800
5.641600 5.943300 6.169000 4.759500 2.569400
1.357100 1.669800 3.212300 5.031900
! phi = 0
8.085900 8.051100 5.023600 3.450800 2.836100
2.192500 1.566200 1.456300 2.039300 1.945200
2.188400 2.921300 3.467500 3.543500 3.374500
3.472300 4.069900 3.615600 2.082200 0.958600
0.792600 1.494200 2.794900 4.853100
! phi = 15
6.639500 5.177400 3.252300 1.952700 1.078400
0.888300 1.505400 2.442300 2.178600 1.578600
1.777400 2.395400 2.820200 2.795200 2.662400
2.917100 2.562100 1.557900 1.322300 1.631400
2.051200 2.555600 3.039100 4.915000
! phi = 30
7.548800 5.095500 2.747000 0.955200 0.444500
1.318700 2.733300 3.223200 2.565500 2.150900
2.394400 2.939300 3.266000 3.210000 3.113400
2.491300 0.978300 0.815300 1.522700 2.055600
2.199900 2.327600 3.474200 7.977800
! phi = 45
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
! phi = 60
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
! phi = 75
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
! phi = 90
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
! phi = 105
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
! phi = 120
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
! phi = 135
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
! phi = 150
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
! phi = 165
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
! glycine map
! mp2/aug-cc-pVDZ//RIMP2/VTZ/VQZ CBS map
C NH1 CT2 C NH1 CT2 C NH1 24
! phi = -180
0.235350 0.182300 0.177200 0.396800 0.859400
1.489700 2.092500 2.297700 1.808600 0.696200
-0.563300 -1.432700 -1.015100 1.426300 -0.564300
0.696200 1.808200 2.301700 2.092600 1.489100
0.859500 0.396900 0.176900 0.182400
! phi = -165
0.020100 -0.203800 -0.269700 0.014200 0.620800
1.392400 2.046200 2.188200 1.683900 0.688500
-0.373700 -0.703500 0.837800 3.704000 -0.730100
0.594100 1.713100 2.205800 2.026400 1.529800
1.027400 0.623800 0.348400 0.182800
! phi = -150
-0.533600 -0.807400 -0.804600 -0.379800 0.365300
1.168000 1.641000 1.618100 1.302200 0.615100
0.065700 0.738500 2.959500 -2.036600 -0.934600
0.407900 1.517000 1.984800 1.833100 1.435200
0.995600 0.562200 0.150600 -0.209000
! phi = -135
-1.208500 -1.429400 -1.319200 -0.817500 -0.112400
0.454400 0.737600 0.879300 0.850100 0.670300
0.943500 -2.651200 -2.829400 -2.199100 -1.065700
0.279600 1.322000 1.668300 1.521300 1.193900
0.765300 0.246000 -0.315500 -0.823200
! phi = -120
-1.789100 -1.965500 -1.860700 -1.447900 -0.896500
-0.401000 -0.015100 0.321300 0.634600 0.976300
-1.977500 -2.883200 -2.848500 -2.137900 -0.960300
0.308700 1.098100 1.245300 1.133600 0.881800
0.448200 -0.153900 -0.823700 -1.404300
! phi = -105
-2.246700 -2.487000 -2.473700 -2.135600 -1.577700
-0.980600 -0.429100 0.144700 0.734000 -0.918300
-2.299200 -2.882200 -2.668600 -1.847100 -0.719800
0.107000 0.496000 0.553500 0.584300 0.494000
0.098300 -0.529800 -1.237900 -1.840100
! phi = -90
-2.851100 -3.181100 -3.199500 -2.785300 -2.054300
-1.242900 -0.476500 0.288100 -0.045300 -1.470600
-2.558800 -2.869400 -2.450300 -1.582200 -0.930800
-0.426400 -0.022700 0.000000 -0.097400 -0.136100
-0.439600 -1.038600 -1.741000 -2.373200
! phi = -75
-3.961800 -4.268200 -4.109000 -3.364700 -2.252200
-1.140400 -0.209800 0.487300 -0.746200 -2.127700
-2.932100 -2.898500 -2.247900 -1.730400 -1.177200
-0.448200 0.034900 -0.073300 -0.531600 -0.933300
-1.360700 -2.009200 -2.745700 -3.424900
! phi = -60
-5.408000 -5.355100 -4.640100 -3.283200 -1.710200
-0.423800 0.354400 -0.103700 -1.577700 -2.828300
-3.151200 -2.649200 -2.183000 -1.761200 -0.981700
-0.174700 0.262600 0.039200 -0.663000 -1.530700
-2.478200 -3.465600 -4.334200 -5.011200
! phi = -45
-6.093200 -5.298400 -3.816620 -1.922530 -0.196160
0.768200 0.568500 -0.831300 -2.343900 -3.037100
-2.663700 -2.191100 -2.022900 -1.438500 -0.649000
0.077000 0.441500 0.257500 -0.491100 -1.820600
-3.473100 -4.895200 -5.790700 -6.205900
! phi = -30
-5.258225 -3.675795 -1.631110 0.430085 1.496470
0.318200 -0.555100 -1.695500 -2.434200 -2.192600
-1.691300 -1.890000 -1.708500 -1.206300 -0.567400
0.054300 0.497200 0.599600 -0.171000 -2.137600
-4.237000 -5.584100 -6.135100 -6.067000
! phi = -15
-3.161820 -0.902080 1.432450 -1.452885 -1.560780
-1.665600 -1.783100 -1.755100 -1.329300 -0.731100
-1.317000 -1.662800 -1.601200 -1.294900 -0.817300
-0.197100 0.549500 0.850400 -0.689700 -2.819900
-4.393000 -5.111500 -5.205690 -4.654785
! phi = 0
0.034035 -2.349860 -3.412065 -3.620070 -3.450950
-2.875650 -1.787800 -0.541250 0.410450 -0.372500
-1.126850 -1.498450 -1.608700 -1.498450 -1.126850
-0.372500 0.410450 -0.541250 -1.787800 -2.875650
-3.450950 -3.620070 -3.412065 -2.349860
! phi = 15
-3.162345 -4.654785 -5.205690 -5.111500 -4.393000
-2.819900 -0.689700 0.850400 0.549500 -0.197100
-0.817300 -1.294900 -1.601200 -1.662800 -1.317000
-0.731100 -1.329300 -1.755100 -1.783100 -1.665600
-1.560780 -1.452885 1.432450 -0.902080
! phi = 30
-5.258220 -6.067000 -6.135100 -5.584100 -4.237000
-2.137600 -0.171000 0.599600 0.497200 0.054300
-0.567400 -1.206300 -1.708500 -1.890000 -1.691300
-2.192600 -2.434200 -1.695500 -0.555100 0.318200
1.496470 0.430085 -1.631110 -3.675795
! phi = 45
-6.093300 -6.205900 -5.790700 -4.895200 -3.473100
-1.820600 -0.491100 0.257500 0.441500 0.077000
-0.649000 -1.438500 -2.022900 -2.191100 -2.663700
-3.037100 -2.343900 -0.831300 0.568500 0.768200
-0.196160 -1.922530 -3.816620 -5.298400
! phi = 60
-5.407500 -5.011200 -4.334200 -3.465600 -2.478200
-1.530700 -0.663000 0.039200 0.262600 -0.174700
-0.981700 -1.761200 -2.183000 -2.649200 -3.151200
-2.828300 -1.577700 -0.103700 0.354400 -0.423800
-1.710200 -3.283200 -4.640100 -5.355100
! phi = 75
-3.961900 -3.424900 -2.745700 -2.009200 -1.360700
-0.933300 -0.531600 -0.073300 0.034900 -0.448200
-1.177200 -1.730400 -2.247900 -2.898500 -2.932100
-2.127700 -0.746200 0.487300 -0.209800 -1.140400
-2.252200 -3.364700 -4.109000 -4.268200
! phi = 90
-2.854500 -2.373200 -1.741000 -1.038600 -0.439600
-0.136100 -0.097400 0.000000 -0.022700 -0.426400
-0.930800 -1.582200 -2.450300 -2.869400 -2.558800
-1.470600 -0.045300 0.288100 -0.476500 -1.242900
-2.054300 -2.785300 -3.199500 -3.181100
! phi = 105
-2.246400 -1.840100 -1.237900 -0.529800 0.098300
0.494000 0.584300 0.553500 0.496000 0.107000
-0.719800 -1.847100 -2.668600 -2.882200 -2.299200
-0.918300 0.734000 0.144700 -0.429100 -0.980600
-1.577700 -2.135600 -2.473700 -2.487000
! phi = 120
-1.788800 -1.404300 -0.823700 -0.153900 0.448200
0.881800 1.133600 1.245300 1.098100 0.308700
-0.960300 -2.137900 -2.848500 -2.883200 -1.977500
0.976300 0.634600 0.321300 -0.015100 -0.401000
-0.896500 -1.447900 -1.860700 -1.965500
! phi = 135
-1.208900 -0.823200 -0.315500 0.246000 0.765300
1.193900 1.521300 1.668300 1.322000 0.279600
-1.065700 -2.199100 -2.829400 -2.651200 0.943500
0.670300 0.850100 0.879300 0.737600 0.454400
-0.112400 -0.817500 -1.319200 -1.429400
! phi = 150
-0.533400 -0.209000 0.150600 0.562200 0.995600
1.435200 1.833100 1.984800 1.517000 0.407900
-0.934600 -2.036600 2.959500 0.738500 0.065700
0.615100 1.302200 1.618100 1.641000 1.168000
0.365300 -0.379800 -0.804600 -0.807400
! phi = 165
0.019900 0.182800 0.348400 0.623800 1.027400
1.529800 2.026400 2.205800 1.713100 0.594100
-0.730100 3.704000 0.837800 -0.703500 -0.373700
0.688500 1.683900 2.188200 2.046200 1.392400
0.620800 0.014200 -0.269700 -0.203800
! glycine before proline map: use glycine map
! mp2/aug-cc-pVDZ//RIMP2/VTZ/VQZ CBS map
C NH1 CT2 C NH1 CT2 C N 24
! phi = -180
0.235350 0.182300 0.177200 0.396800 0.859400
1.489700 2.092500 2.297700 1.808600 0.696200
-0.563300 -1.432700 -1.015100 1.426300 -0.564300
0.696200 1.808200 2.301700 2.092600 1.489100
0.859500 0.396900 0.176900 0.182400
! phi = -165
0.020100 -0.203800 -0.269700 0.014200 0.620800
1.392400 2.046200 2.188200 1.683900 0.688500
-0.373700 -0.703500 0.837800 3.704000 -0.730100
0.594100 1.713100 2.205800 2.026400 1.529800
1.027400 0.623800 0.348400 0.182800
! phi = -150
-0.533600 -0.807400 -0.804600 -0.379800 0.365300
1.168000 1.641000 1.618100 1.302200 0.615100
0.065700 0.738500 2.959500 -2.036600 -0.934600
0.407900 1.517000 1.984800 1.833100 1.435200
0.995600 0.562200 0.150600 -0.209000
! phi = -135
-1.208500 -1.429400 -1.319200 -0.817500 -0.112400
0.454400 0.737600 0.879300 0.850100 0.670300
0.943500 -2.651200 -2.829400 -2.199100 -1.065700
0.279600 1.322000 1.668300 1.521300 1.193900
0.765300 0.246000 -0.315500 -0.823200
! phi = -120
-1.789100 -1.965500 -1.860700 -1.447900 -0.896500
-0.401000 -0.015100 0.321300 0.634600 0.976300
-1.977500 -2.883200 -2.848500 -2.137900 -0.960300
0.308700 1.098100 1.245300 1.133600 0.881800
0.448200 -0.153900 -0.823700 -1.404300
! phi = -105
-2.246700 -2.487000 -2.473700 -2.135600 -1.577700
-0.980600 -0.429100 0.144700 0.734000 -0.918300
-2.299200 -2.882200 -2.668600 -1.847100 -0.719800
0.107000 0.496000 0.553500 0.584300 0.494000
0.098300 -0.529800 -1.237900 -1.840100
! phi = -90
-2.851100 -3.181100 -3.199500 -2.785300 -2.054300
-1.242900 -0.476500 0.288100 -0.045300 -1.470600
-2.558800 -2.869400 -2.450300 -1.582200 -0.930800
-0.426400 -0.022700 0.000000 -0.097400 -0.136100
-0.439600 -1.038600 -1.741000 -2.373200
! phi = -75
-3.961800 -4.268200 -4.109000 -3.364700 -2.252200
-1.140400 -0.209800 0.487300 -0.746200 -2.127700
-2.932100 -2.898500 -2.247900 -1.730400 -1.177200
-0.448200 0.034900 -0.073300 -0.531600 -0.933300
-1.360700 -2.009200 -2.745700 -3.424900
! phi = -60
-5.408000 -5.355100 -4.640100 -3.283200 -1.710200
-0.423800 0.354400 -0.103700 -1.577700 -2.828300
-3.151200 -2.649200 -2.183000 -1.761200 -0.981700
-0.174700 0.262600 0.039200 -0.663000 -1.530700
-2.478200 -3.465600 -4.334200 -5.011200
! phi = -45
-6.093200 -5.298400 -3.816620 -1.922530 -0.196160
0.768200 0.568500 -0.831300 -2.343900 -3.037100
-2.663700 -2.191100 -2.022900 -1.438500 -0.649000
0.077000 0.441500 0.257500 -0.491100 -1.820600
-3.473100 -4.895200 -5.790700 -6.205900
! phi = -30
-5.258225 -3.675795 -1.631110 0.430085 1.496470
0.318200 -0.555100 -1.695500 -2.434200 -2.192600
-1.691300 -1.890000 -1.708500 -1.206300 -0.567400
0.054300 0.497200 0.599600 -0.171000 -2.137600
-4.237000 -5.584100 -6.135100 -6.067000
! phi = -15
-3.161820 -0.902080 1.432450 -1.452885 -1.560780
-1.665600 -1.783100 -1.755100 -1.329300 -0.731100
-1.317000 -1.662800 -1.601200 -1.294900 -0.817300
-0.197100 0.549500 0.850400 -0.689700 -2.819900
-4.393000 -5.111500 -5.205690 -4.654785
! phi = 0
0.034035 -2.349860 -3.412065 -3.620070 -3.450950
-2.875650 -1.787800 -0.541250 0.410450 -0.372500
-1.126850 -1.498450 -1.608700 -1.498450 -1.126850
-0.372500 0.410450 -0.541250 -1.787800 -2.875650
-3.450950 -3.620070 -3.412065 -2.349860
! phi = 15
-3.162345 -4.654785 -5.205690 -5.111500 -4.393000
-2.819900 -0.689700 0.850400 0.549500 -0.197100
-0.817300 -1.294900 -1.601200 -1.662800 -1.317000
-0.731100 -1.329300 -1.755100 -1.783100 -1.665600
-1.560780 -1.452885 1.432450 -0.902080
! phi = 30
-5.258220 -6.067000 -6.135100 -5.584100 -4.237000
-2.137600 -0.171000 0.599600 0.497200 0.054300
-0.567400 -1.206300 -1.708500 -1.890000 -1.691300
-2.192600 -2.434200 -1.695500 -0.555100 0.318200
1.496470 0.430085 -1.631110 -3.675795
! phi = 45
-6.093300 -6.205900 -5.790700 -4.895200 -3.473100
-1.820600 -0.491100 0.257500 0.441500 0.077000
-0.649000 -1.438500 -2.022900 -2.191100 -2.663700
-3.037100 -2.343900 -0.831300 0.568500 0.768200
-0.196160 -1.922530 -3.816620 -5.298400
! phi = 60
-5.407500 -5.011200 -4.334200 -3.465600 -2.478200
-1.530700 -0.663000 0.039200 0.262600 -0.174700
-0.981700 -1.761200 -2.183000 -2.649200 -3.151200
-2.828300 -1.577700 -0.103700 0.354400 -0.423800
-1.710200 -3.283200 -4.640100 -5.355100
! phi = 75
-3.961900 -3.424900 -2.745700 -2.009200 -1.360700
-0.933300 -0.531600 -0.073300 0.034900 -0.448200
-1.177200 -1.730400 -2.247900 -2.898500 -2.932100
-2.127700 -0.746200 0.487300 -0.209800 -1.140400
-2.252200 -3.364700 -4.109000 -4.268200
! phi = 90
-2.854500 -2.373200 -1.741000 -1.038600 -0.439600
-0.136100 -0.097400 0.000000 -0.022700 -0.426400
-0.930800 -1.582200 -2.450300 -2.869400 -2.558800
-1.470600 -0.045300 0.288100 -0.476500 -1.242900
-2.054300 -2.785300 -3.199500 -3.181100
! phi = 105
-2.246400 -1.840100 -1.237900 -0.529800 0.098300
0.494000 0.584300 0.553500 0.496000 0.107000
-0.719800 -1.847100 -2.668600 -2.882200 -2.299200
-0.918300 0.734000 0.144700 -0.429100 -0.980600
-1.577700 -2.135600 -2.473700 -2.487000
! phi = 120
-1.788800 -1.404300 -0.823700 -0.153900 0.448200
0.881800 1.133600 1.245300 1.098100 0.308700
-0.960300 -2.137900 -2.848500 -2.883200 -1.977500
0.976300 0.634600 0.321300 -0.015100 -0.401000
-0.896500 -1.447900 -1.860700 -1.965500
! phi = 135
-1.208900 -0.823200 -0.315500 0.246000 0.765300
1.193900 1.521300 1.668300 1.322000 0.279600
-1.065700 -2.199100 -2.829400 -2.651200 0.943500
0.670300 0.850100 0.879300 0.737600 0.454400
-0.112400 -0.817500 -1.319200 -1.429400
! phi = 150
-0.533400 -0.209000 0.150600 0.562200 0.995600
1.435200 1.833100 1.984800 1.517000 0.407900
-0.934600 -2.036600 2.959500 0.738500 0.065700
0.615100 1.302200 1.618100 1.641000 1.168000
0.365300 -0.379800 -0.804600 -0.807400
! phi = 165
0.019900 0.182800 0.348400 0.623800 1.027400
1.529800 2.026400 2.205800 1.713100 0.594100
-0.730100 3.704000 0.837800 -0.703500 -0.373700
0.688500 1.683900 2.188200 2.046200 1.392400
0.620800 0.014200 -0.269700 -0.203800
NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
!adm jr., 2013 correction
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
!
!carbons
C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO
! NMA pure solvent, adm jr., 3/3/93
CA 0.000000 -0.070000 1.992400 ! ALLOW ARO
! benzene (JES)
CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO
! adm jr. 3/3/92, acetic acid heat of solvation
CD 0.000000 -0.070000 2.000000 ! ALLOW POL
! adm jr. 3/19/92, acetate a.i. and dH of solvation
CE1 0.000000 -0.068000 2.090000 !
! for propene, yin/adm jr., 12/95
CE2 0.000000 -0.064000 2.080000 !
! for ethene, yin/adm jr., 12/95
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
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
CS 0.000000 -0.110000 2.200000 ! ALLOW SUL
! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92
CPT 0.000000 -0.099000 1.860000 ! atm, indole vaporization 5/05
CY 0.000000 -0.073000 1.990000 ! atm, indole vaporization 5/05
CAI 0.000000 -0.073000 1.990000 ! atm, indole vaporization 5/05
! TRP, JWK 08/29/89
!new alkanes atoms types for conversion to new LJ parameters for c27
CT 0.0 -0.0200 2.275 0.0 -0.01 1.9 !
CT1 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! alkane, 4/07, viv and adm jr.
CT2 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
CT2A 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! from CT2 (GLU, HSP), 05282010, zhu
CT3 0.0 -0.0780 2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
! hydrogens
H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC
! same as TIP3P hydrogen, adm jr., 7/20/89
HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC
! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92
HB1 0.000000 -0.022000 1.320000 !
! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92
HB2 0.000000 -0.028000 1.340000 !
! Yin and MacKerell, adm jr., 5/30/02
HE1 0.000000 -0.031000 1.250000 !
! for propene, yin/adm jr., 12/95
HE2 0.000000 -0.026000 1.260000 !
! for ethene, yin/adm jr., 12/95
!HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC
! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92
HC 0.000000 -0.046000 0.224500 ! ALLOW POL
! new, small polar Hydrogen, see also adm jr. JG 8/27/89
HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! ALLOW ARO
! JES 8/25/89 values from Jorgensen fit to hydration energy
HR1 0.000000 -0.046000 0.900000 ! ALLOW ARO
! adm jr., 6/27/90, his
HR2 0.000000 -0.046000 0.700000 ! ALLOW ARO
! adm jr., 6/27/90, his
HR3 0.000000 -0.007800 1.468000 ! ALLOW ARO
! adm jr., 3/24/92, maintain old aliphatic H VDW params
HS 0.000000 -0.100000 0.450000 ! ALLOW SUL
! methanethiol pure solvent, adm jr., 6/22/92
!new alkanes atoms types for conversion to new LJ parameters for c27 (see toppar_all22_prot_aliphatic_c27.str)
HA1 0.0 -0.045 1.3400 ! alkane, viv and adm jr., 4/07
HA2 0.0 -0.034 1.3400 ! alkane, viv and adm jr., 4/07
HA3 0.0 -0.024 1.3400 ! alkane, yin and mackerell, 4/98
!nitrogens
N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 ! ALLOW PRO
! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
NC2 0.000000 -0.200000 1.850000 ! ALLOW POL
! JG 8/27/89; note: NH1 in ARG was changed to NC2.
NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO
! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK)
NH2 0.000000 -0.200000 1.850000 ! ALLOW POL
! adm jr.
NH3 0.000000 -0.200000 1.850000 ! ALLOW POL
! adm jr.
NP 0.000000 -0.200000 1.850000 ! ALLOW PRO
! N-terminal proline; from 6-31g* +ProNH2 RLD 9/28/90
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 ! atm, indole vaporization 5/05
! oxygens
O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL
! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK)
OB 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ARO
! adm jr., 10/17/90, acetic acid carbonyl O
OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION
! JG 8/27/89
OH1 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO
! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P)
OS 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO
! adm jr. 9/17/90, avoid O* wildcard
! sulfurs
S 0.000000 -0.450000 2.000000 ! ALLOW SUL ION
! adm jr., 3/3/92, methanethiol/ethylmethylsulfide pure solvent
SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION
! adm jr., 3/3/92, dimethyldisulphide pure solvent
SS 0.000000 -0.470000 2.200000 ! ALLOW SUL
! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92
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/toppar_water_ions.str 0 → 100644
View file @ c7aa1d00
* Toplogy and parameter information for water and ions.
*
!Testcase
!test_water_ions.inp
! IMPORTANT NOTE: this file contains NBFixes between carboxylates and sodium,
! which will only apply if the main files containing carboxylate atom types
! have been read in first!
!references
!
!TIP3P water model
!
!W.L. Jorgensen; J.Chandrasekhar; J.D. Madura; R.W. Impey;
!M.L. Klein; "Comparison of simple potential functions for
!simulating liquid water", J. Chem. Phys. 79 926-935 (1983).
!
!IONS
!
!Ions from Roux and coworkers
!
!Beglov, D. and Roux, B., Finite Representation of an Infinite
!Bulk System: Solvent Boundary Potential for Computer Simulations,
!Journal of Chemical Physics, 1994, 100: 9050-9063
!
!ZINC
!
!Stote, R.H. and Karplus, M. Zinc Binding in Proteins and
!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS:
!Structure, Function, and Genetics 23:12-31 (1995)
!test "append" to determine if previous toppar files have been read and
!add append to "read rtf card" if true
set nat ?NATC
set app
!We're exploiting what is arguably a bug in the parser. On the left hand side,
!the quotes have priority, so NAT is correctly substituted. On the right hand
!side, the ? has priority and NATC" (sic) is not a valid substitution...
if "@NAT" ne "?NATC" if @nat ne 0 set app append
read rtf card @app
* Topology for water and ions
*
31 1
MASS 1 HT 1.00800 H ! TIPS3P WATER HYDROGEN
MASS 2 HX 1.00800 H ! hydroxide hydrogen
MASS 3 OT 15.99940 O ! TIPS3P WATER OXYGEN
MASS 4 OX 15.99940 O ! hydroxide oxygen
MASS 5 LIT 6.94100 LI ! Lithium ion
MASS 6 SOD 22.98977 NA ! Sodium Ion
MASS 7 MG 24.30500 MG ! Magnesium Ion
MASS 8 POT 39.09830 K ! Potassium Ion
MASS 9 CAL 40.08000 CA ! Calcium Ion
MASS 10 RUB 85.46780 RB ! Rubidium Ion
MASS 11 CES 132.90545 CS ! Cesium Ion
MASS 12 BAR 137.32700 BA ! Barium Ion
MASS 13 ZN 65.37000 ZN ! zinc (II) cation
MASS 14 CAD 112.41100 CD ! cadmium (II) cation
MASS 15 CLA 35.45000 CL ! Chloride Ion
default first none last none
RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral
GROUP
ATOM OH2 OT -0.834
ATOM H1 HT 0.417
ATOM H2 HT 0.417
BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake
ANGLE H1 OH2 H2 ! required
DONOR H1 OH2
DONOR H2 OH2
ACCEPTOR OH2
PATCHING FIRS NONE LAST NONE
RESI TP3M 0.000 ! "mmff" water model, as an analog of tip3p
GROUP
ATOM OH2 OT -0.834 ! these charges are replaced by the mmff setup
ATOM H1 HT 0.417 ! these charges are replaced by the mmff setup
ATOM H2 HT 0.417 ! these charges are replaced by the mmff setup
BOND OH2 H1 OH2 H2 ! omits the H1-H2 bond, which is needed for shake with tip3p
ANGLE H1 OH2 H2 ! required
DONOR H1 OH2
DONOR H2 OH2
ACCEPTOR OH2
PATCHING FIRS NONE LAST NONE
RESI OH -1.00 ! hydroxide ion by adm.jr.
GROUP
ATOM O1 OX -1.32
ATOM H1 HX 0.32
BOND O1 H1
DONOR H1 O1
ACCEPTOR O1
! Ion parameters from Benoit Roux and Coworkers
! As of 8/10 new NBFIX terms required
!
RESI LIT 1.00 ! Lithium Ion
GROUP
ATOM LIT LIT 1.00
PATCHING FIRST NONE LAST NONE
RESI SOD 1.00 ! Sodium Ion
GROUP
ATOM SOD SOD 1.00
PATCHING FIRST NONE LAST NONE
RESI MG 2.00 ! Magnesium Ion
GROUP
ATOM MG MG 2.00
PATCHING FIRST NONE LAST NONE
RESI POT 1.00 ! Potassium Ion
GROUP
ATOM POT POT 1.00
PATCHING FIRST NONE LAST NONE
RESI CAL 2.00 ! Calcium Ion
GROUP
ATOM CAL CAL 2.00
PATCHING FIRST NONE LAST NONE
RESI RUB 1.00 ! Rubidium Ion
GROUP
ATOM RUB RUB 1.00
PATCHING FIRST NONE LAST NONE
RESI CES 1.00 ! Cesium Ion
GROUP
ATOM CES CES 1.00
PATCHING FIRST NONE LAST NONE
RESI BAR 2.00 ! Barium Ion
GROUP
ATOM BAR BAR 2.00
PATCHING FIRST NONE LAST NONE
RESI ZN2 2.00 ! Zinc (II) cation, Roland Stote
GROUP
ATOM ZN ZN 2.00
PATCHING FIRST NONE LAST NONE
RESI CD2 2.00 ! Cadmium (II) cation
GROUP
ATOM CD CAD 2.00
PATCHING FIRST NONE LAST NONE
RESI CLA -1.00 ! Chloride Ion
GROUP
ATOM CLA CLA -1.00
PATCHING FIRST NONE LAST NONE
END
read para card flex @app
* Parameters for water and ions
*
ATOMS
MASS 1 HT 1.00800 ! TIPS3P WATER HYDROGEN
MASS 2 HX 1.00800 ! hydroxide hydrogen
MASS 3 OT 15.99940 ! TIPS3P WATER OXYGEN
MASS 4 OX 15.99940 ! hydroxide oxygen
MASS 5 LIT 6.94100 ! Lithium ion
MASS 6 SOD 22.98977 ! Sodium Ion
MASS 7 MG 24.30500 ! Magnesium Ion
MASS 8 POT 39.09830 ! Potassium Ion
MASS 9 CAL 40.08000 ! Calcium Ion
MASS 10 RUB 85.46780 ! Rubidium Ion
MASS 11 CES 132.90545 ! Cesium Ion
MASS 12 BAR 137.32700 ! Barium Ion
MASS 13 ZN 65.37000 ! zinc (II) cation
MASS 14 CAD 112.41100 ! cadmium (II) cation
MASS 15 CLA 35.45000 ! Chloride Ion
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb b0
!
HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM)
HT OT 450.0 0.9572 ! from TIPS3P geometry
OX HX 545.0 0.9700 ! hydroxide ion
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
!
HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY
DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types Kchi n delta
!
!
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
!
NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
!TIP3P LJ parameters
HT 0.0 -0.046 0.2245
OT 0.0 -0.1521 1.7682
!for hydroxide
OX 0.000000 -0.120000 1.700000 ! ALLOW POL ION
! JG 8/27/89
HX 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC
! same as TIP3P hydrogen, adm jr., 7/20/89
!ions
LIT 0.0 -0.00233 1.2975 ! Lithium
! From S Noskov, target ddG(Li-Na) was 23-26.0 kcal/mol (see JPC B, Lamoureux&Roux,2006)
SOD 0.0 -0.0469 1.41075 ! new CHARMM Sodium
! ddG of -18.6 kcal/mol with K+ from S. Noskov
MG 0.0 -0.0150 1.18500 ! Magnesium
! B. Roux dA = -441.65
POT 0.0 -0.0870 1.76375 ! Potassium
! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol
CAL 0.0 -0.120 1.367 ! Calcium
! S. Marchand and B. Roux, dA = -384.8 kcal/mol
RUB 0.0000 -0.15 1.90 ! Rubidium
! delta A with respect to POT is +6.0 kcal/mol in bulk water
CES 0.0 -0.1900 2.100 ! Cesium
! delta A with respect to POT is +12.0 kcal/mol
BAR 0.0 -0.150 1.890 ! Barium
! B. Roux, dA = dA[calcium] + 64.2 kcal/mol
ZN 0.000000 -0.250000 1.090000 ! Zinc
! RHS March 18, 1990
CAD 0.000000 -0.120000 1.357000 ! Cadmium
! S. Marchand and B. Roux, from delta delta G
CLA 0.0 -0.150 2.27 ! Chloride
! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol
NBFIX
! Emin Rmin
! (kcal/mol) (A)
SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189
POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189
END
! The following section contains NBFixes for sodium interacting with
! carboxylate oxygens of various CHARMM force fields. It will generate
! level -1 warnings whenever any of these force fields have not been
! read prior to the current stream file. Since we don't want to force
! the user to always read all the force fields, we're suppressing the
! warnings. The only side effect is that you will have "most severe
! warning was at level 0" at the end of your output. Also note that
! the user is responsible for reading the current file last if they
! want the NBFixes to apply. A more elegant solution would require new
! features to be added to CHARMM.
! parallel fix, to avoid duplicated messages in the log
set para
if ?NUMNODE gt 1 set para node 0
set wrn ?WRNLEV
! Some versions of CHARMM don't seem to initialize wrnlev...
if "@WRN" eq "?WRNLEV" set wrn 5
set bom ?bomlev
WRNLEV -1 @PARA
BOMLEV -1 @PARA
read para card flex append
* NBFix between carboxylate and sodium
*
! These NBFixes will only apply if the main files have been read in first!!!
NBFIX
!new SOD NBFIX values
! Simulations of Anionic Lipid Membranes: Development of Interaction-Specific
! Ion Parameters and Validation using NMR Data.
! Venable, R.M.; Luo, Y,; Gawrisch, K.; Roux, B.; Pastor, R.W.
! J. Phys. Chem. B 2013, 117 (35), pp 10183–10192. DOI: 10.1021/jp401512z
!
SOD OCL -0.07502 3.23 ! osmotic P; carboxylate =O
SOD OBL -0.07502 3.13 ! POPC optim.; ester =O
SOD O2L -0.07502 3.16 ! POPC optim.; phosphate =O
!
SOD OC -0.07502 3.23 ! For prot carboxylate groups
SOD OC2D2 -0.07502 3.23 ! For carb carboxylate groups
SOD OG2D2 -0.07502 3.23 ! For CGenFF carboxylate groups
END
BOMLEV @bom @PARA
WRNLEV @wrn @PARA
return
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