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Commit 2a2fae31 authored by peastman's avatar peastman
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Merge pull request #549 from swails/charmm_nbfix 

Add NBFIX support to CHARMM parsers
parents 213c77eb 920ddf97
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wrappers/python/CMakeLists.txt
View file @ 2a2fae31
......@@ -55,13 +55,16 @@ foreach(SUBDIR ${SUBDIRS})
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.xml"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.pdb"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prmtop"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prm"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.inpcrd"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.crd"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.parm7"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.rst7"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.ncrst"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.dms"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.top"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.par"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.str"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*psf"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/charmm22.*"
)
......
wrappers/python/simtk/openmm/app/__init__.py
View file @ 2a2fae31
......@@ -28,7 +28,7 @@ from desmonddmsfile import DesmondDMSFile
from checkpointreporter import CheckpointReporter
from charmmcrdfiles import CharmmCrdFile, CharmmRstFile
from charmmparameterset import CharmmParameterSet
from charmmpsffile import CharmmPsfFile
from charmmpsffile import CharmmPsfFile, CharmmPSFWarning
# Enumerated values
......
wrappers/python/simtk/openmm/app/charmmparameterset.py
View file @ 2a2fae31
......@@ -13,7 +13,7 @@ Copyright (c) 2014 the Authors
Author: Jason M. Swails
Contributors:
Date: April 18, 2014
Date: July 17, 2014
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
......@@ -123,6 +123,8 @@ class CharmmParameterSet(object):
elif arg.endswith('.str'):
strs.append(arg)
elif arg.endswith('.inp'):
# Only consider the file name (since the directory is likely
# "toppar" and will screw up file type detection)
fname = os.path.split(arg)[1]
if 'par' in fname:
pars.append(arg)
......@@ -436,11 +438,29 @@ class CharmmParameterSet(object):
try:
at1 = words[0]
at2 = words[1]
emin = conv(words[2], float, 'NBFIX Emin')
emin = abs(conv(words[2], float, 'NBFIX Emin'))
rmin = conv(words[3], float, 'NBFIX Rmin')
try:
emin14 = abs(conv(words[4], float, 'NBFIX Emin 1-4'))
rmin14 = conv(words[5], float, 'NBFIX Rmin 1-4')
except IndexError:
emin14 = rmin14 = None
try:
self.atom_types_str[at1].add_nbfix(at2, rmin, emin,
rmin14, emin14)
self.atom_types_str[at2].add_nbfix(at1, rmin, emin,
rmin14, emin14)
except KeyError:
# Some stream files define NBFIX terms with an atom that
# is defined in another toppar file that does not
# necessarily have to be loaded. As a result, not every
# NBFIX found here will necessarily need to be applied.
# If we can't find a particular atom type, don't bother
# adding that nbfix and press on
pass
except IndexError:
raise CharmmFileError('Could not parse NBFIX terms.')
self.nbfix_types[(min(at1, at2), max(at1, at2))] = (emin, rmin)
self.nbfix_types[(min(at1, at2), max(at1, at2))] = (rmin, emin)
# Now we're done. Load the nonbonded types into the relevant AtomType
# instances. In order for this to work, all keys in nonbonded_types
# must be in the self.atom_types_str dict. Raise a RuntimeError if this
......
wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ 2a2fae31
......@@ -995,11 +995,25 @@ class CharmmPsfFile(object):
u.kilojoule_per_mole)
ene_conv = dihe_frc_conv
# Create the system
# Create the system and determine if any of our atoms have NBFIX (and
# therefore requires a CustomNonbondedForce instead)
typenames = set()
system = mm.System()
if verbose: print('Adding particles...')
for atom in self.atom_list:
typenames.add(atom.type.name)
system.addParticle(atom.mass)
has_nbfix_terms = False
typenames = list(typenames)
try:
for i, typename in enumerate(typenames):
typ = params.atom_types_str[typename]
for j in range(i, len(typenames)):
if typenames[j] in typ.nbfix:
has_nbfix_terms = True
raise StopIteration
except StopIteration:
pass
# Set up the constraints
if verbose and (constraints is not None and not rigidWater):
print('Adding constraints...')
......@@ -1240,9 +1254,85 @@ class CharmmPsfFile(object):
# Add per-particle nonbonded parameters (LJ params)
sigma_scale = 2**(-1/6) * 2
for i, atm in enumerate(self.atom_list):
if not has_nbfix_terms:
for atm in self.atom_list:
force.addParticle(atm.charge, sigma_scale*atm.type.rmin*length_conv,
abs(atm.type.epsilon*ene_conv))
else:
for atm in self.atom_list:
force.addParticle(atm.charge, 1.0, 0.0)
# Now add the custom nonbonded force that implements NBFIX. First
# thing we need to do is condense our number of types
lj_idx_list = [0 for atom in self.atom_list]
lj_radii, lj_depths = [], []
num_lj_types = 0
lj_type_list = []
for i, atom in enumerate(self.atom_list):
atom = atom.type
if lj_idx_list[i]: continue # already assigned
num_lj_types += 1
lj_idx_list[i] = num_lj_types
ljtype = (atom.rmin, atom.epsilon)
lj_type_list.append(atom)
lj_radii.append(atom.rmin)
lj_depths.append(atom.epsilon)
for j in range(i+1, len(self.atom_list)):
atom2 = self.atom_list[j].type
if lj_idx_list[j] > 0: continue # already assigned
if atom2 is atom:
lj_idx_list[j] = num_lj_types
elif not atom.nbfix:
# Only non-NBFIXed atom types can be compressed
ljtype2 = (atom2.rmin, atom2.epsilon)
if ljtype == ljtype2:
lj_idx_list[j] = num_lj_types
# Now everything is assigned. Create the A-coefficient and
# B-coefficient arrays
acoef = [0 for i in range(num_lj_types*num_lj_types)]
bcoef = acoef[:]
for i in range(num_lj_types):
for j in range(num_lj_types):
namej = lj_type_list[j].name
try:
rij, wdij, rij14, wdij14 = lj_type_list[i].nbfix[namej]
except KeyError:
rij = (lj_radii[i] + lj_radii[j]) * length_conv
wdij = sqrt(lj_depths[i] * lj_depths[j]) * ene_conv
else:
rij *= length_conv
wdij *= ene_conv
acoef[i+num_lj_types*j] = sqrt(wdij) * rij**6
bcoef[i+num_lj_types*j] = 2 * wdij * rij**6
cforce = mm.CustomNonbondedForce('(a/r6)^2-b/r6; r6=r^6;'
'a=acoef(type1, type2);'
'b=bcoef(type1, type2)')
cforce.addTabulatedFunction('acoef',
mm.Discrete2DFunction(num_lj_types, num_lj_types, acoef))
cforce.addTabulatedFunction('bcoef',
mm.Discrete2DFunction(num_lj_types, num_lj_types, bcoef))
cforce.addPerParticleParameter('type')
cforce.setForceGroup(self.NONBONDED_FORCE_GROUP)
if (nonbondedMethod is ff.PME or nonbondedMethod is ff.Ewald or
nonbondedMethod is ff.CutoffPeriodic):
cforce.setNonbondedMethod(cforce.CutoffPeriodic)
cforce.setCutoffDistance(nonbondedCutoff)
cforce.setUseLongRangeCorrection(True)
elif nonbondedMethod is ff.NoCutoff:
cforce.setNonbondedMethod(cforce.NoCutoff)
elif nonbondedMethod is ff.CutoffNonPeriodic:
cforce.setNonbondedMethod(cforce.CutoffNonPeriodic)
cforce.setCutoffDistance(nonbondedCutoff)
else:
raise ValueError('Unrecognized nonbonded method')
if switchDistance and nonbondedMethod is not ff.NoCutoff:
# make sure it's legal
if switchDistance >= nonbondedCutoff:
raise ValueError('switchDistance is too large compared '
'to the cutoff!')
cforce.setUseSwitchingFunction(True)
cforce.setSwitchingDistance(switchDistance)
for i in lj_idx_list:
cforce.addParticle((i - 1,)) # adjust for indexing from 0
# Add 1-4 interactions
excluded_atom_pairs = set() # save these pairs so we don't zero them out
......@@ -1283,6 +1373,13 @@ class CharmmPsfFile(object):
continue
force.addException(atom.idx, atom2.idx, 0.0, 0.1, 0.0)
system.addForce(force)
# If we needed a CustomNonbondedForce, map all of the exceptions from
# the NonbondedForce to the CustomNonbondedForce
if has_nbfix_terms:
for i in range(force.getNumExceptions()):
ii, jj, q, eps, sig = force.getExceptionParameters(i)
cforce.addExclusion(ii, jj)
system.addForce(cforce)
# Add GB model if we're doing one
if implicitSolvent is not None:
......
wrappers/python/simtk/openmm/app/internal/charmm/_charmmfile.py
View file @ 2a2fae31
......@@ -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 @ 2a2fae31
......@@ -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/tests/TestCharmmFiles.py
View file @ 2a2fae31
......@@ -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/ala3_solv.crd 0 → 100644
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wrappers/python/tests/systems/ala3_solv.psf 0 → 100644
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wrappers/python/tests/systems/par_all36_prot.prm 0 → 100644
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wrappers/python/tests/systems/toppar_water_ions.str 0 → 100644
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* 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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