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Commit 86d8dbf9 authored by John Chodera (MSKCC)'s avatar John Chodera (MSKCC)
Browse files

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

parents 818db2b2 0bdeeb0e
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Showing with 355 additions and 295 deletions
wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ 86d8dbf9
......@@ -32,9 +32,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
from __future__ import division
from __future__ import absolute_import
from __future__ import print_function
from __future__ import division, absolute_import, print_function
from functools import wraps
from math import pi, cos, sin, sqrt
......@@ -666,88 +664,6 @@ class CharmmPsfFile(object):
return topology
def _get_gb_params(self, gb_model=HCT):
""" Gets the GB parameters. Need this method to special-case GB neck """
screen = [0 for atom in self.atom_list]
if gb_model is GBn:
radii = _bondi_radii(self.atom_list)
screen = [0.5 for atom in self.atom_list]
for i, atom in enumerate(self.atom_list):
if atom.type.atomic_number == 6:
screen[i] = 0.48435382330
elif atom.type.atomic_number == 1:
screen[i] = 1.09085413633
elif atom.type.atomic_number == 7:
screen[i] = 0.700147318409
elif atom.type.atomic_number == 8:
screen[i] = 1.06557401132
elif atom.type.atomic_number == 16:
screen[i] = 0.602256336067
elif gb_model is GBn2:
radii = _mbondi3_radii(self.atom_list)
# Add non-optimized values as defaults
alpha = [1.0 for i in self.atom_list]
beta = [0.8 for i in self.atom_list]
gamma = [4.85 for i in self.atom_list]
screen = [0.5 for i in self.atom_list]
for i, atom in enumerate(self.atom_list):
if atom.type.atomic_number == 6:
screen[i] = 1.058554
alpha[i] = 0.733756
beta[i] = 0.506378
gamma[i] = 0.205844
elif atom.type.atomic_number == 1:
screen[i] = 1.425952
alpha[i] = 0.788440
beta[i] = 0.798699
gamma[i] = 0.437334
elif atom.type.atomic_number == 7:
screen[i] = 0.733599
alpha[i] = 0.503364
beta[i] = 0.316828
gamma[i] = 0.192915
elif atom.type.atomic_number == 8:
screen[i] = 1.061039
alpha[i] = 0.867814
beta[i] = 0.876635
gamma[i] = 0.387882
elif atom.type.atomic_number == 16:
screen[i] = -0.703469
alpha[i] = 0.867814
beta[i] = 0.876635
gamma[i] = 0.387882
else:
# Set the default screening parameters
for i, atom in enumerate(self.atom_list):
if atom.type.atomic_number == 1:
screen[i] = 0.85
elif atom.type.atomic_number == 6:
screen[i] = 0.72
elif atom.type.atomic_number == 7:
screen[i] = 0.79
elif atom.type.atomic_number == 8:
screen[i] = 0.85
elif atom.type.atomic_number == 9:
screen[i] = 0.88
elif atom.type.atomic_number == 15:
screen[i] = 0.86
elif atom.type.atomic_number == 16:
screen[i] = 0.96
else:
screen[i] = 0.8
# Determine which radii set we need
if gb_model is OBC1 or gb_model is OBC2:
radii = _mbondi2_radii(self.atom_list)
elif gb_model is HCT:
radii = _mbondi_radii(self.atom_list)
length_conv = u.angstrom.conversion_factor_to(u.nanometer)
radii = [x * length_conv for x in radii]
if gb_model is GBn2:
return zip(radii, screen, alpha, beta, gamma)
return zip(radii, screen)
def createSystem(self, params, nonbondedMethod=ff.NoCutoff,
nonbondedCutoff=1.0*u.nanometer,
switchDistance=0.0*u.nanometer,
......@@ -1249,8 +1165,6 @@ class CharmmPsfFile(object):
# Add GB model if we're doing one
if implicitSolvent is not None:
if verbose: print('Adding GB parameters...')
gb_parms = self._get_gb_params(implicitSolvent)
# If implicitSolventKappa is None, compute it from salt
# concentration
if implicitSolventKappa is None:
......@@ -1289,6 +1203,7 @@ class CharmmPsfFile(object):
elif implicitSolvent is GBn2:
gb = GBSAGBn2Force(solventDielectric, soluteDielectric, None,
cutoff, kappa=implicitSolventKappa)
gb_parms = gb.getStandardParameters(self.topology)
for atom, gb_parm in zip(self.atom_list, gb_parms):
gb.addParticle([atom.charge] + list(gb_parm))
# Set cutoff method
......
wrappers/python/simtk/openmm/app/gromacstopfile.py
View file @ 86d8dbf9
......@@ -259,7 +259,7 @@ class GromacsTopFile(object):
"""Process the [ defaults ] line."""
fields = line.split()
if len(fields) < 4:
raise ValueError('Too few fields in [ defaults ] line: '+line);
raise ValueError('Too few fields in [ defaults ] line: '+line)
if fields[0] != '1':
raise ValueError('Unsupported nonbonded type: '+fields[0])
if fields[1] != '2':
......@@ -272,7 +272,7 @@ class GromacsTopFile(object):
"""Process a line in the [ moleculetypes ] category."""
fields = line.split()
if len(fields) < 1:
raise ValueError('Too few fields in [ moleculetypes ] line: '+line);
raise ValueError('Too few fields in [ moleculetypes ] line: '+line)
type = GromacsTopFile._MoleculeType()
self._moleculeTypes[fields[0]] = type
self._currentMoleculeType = type
......@@ -281,7 +281,7 @@ class GromacsTopFile(object):
"""Process a line in the [ molecules ] category."""
fields = line.split()
if len(fields) < 2:
raise ValueError('Too few fields in [ molecules ] line: '+line);
raise ValueError('Too few fields in [ molecules ] line: '+line)
self._molecules.append((fields[0], int(fields[1])))
def _processAtom(self, line):
......@@ -290,7 +290,7 @@ class GromacsTopFile(object):
raise ValueError('Found [ atoms ] section before [ moleculetype ]')
fields = line.split()
if len(fields) < 5:
raise ValueError('Too few fields in [ atoms ] line: '+line);
raise ValueError('Too few fields in [ atoms ] line: '+line)
self._currentMoleculeType.atoms.append(fields)
def _processBond(self, line):
......@@ -299,9 +299,9 @@ class GromacsTopFile(object):
raise ValueError('Found [ bonds ] section before [ moleculetype ]')
fields = line.split()
if len(fields) < 3:
raise ValueError('Too few fields in [ bonds ] line: '+line);
raise ValueError('Too few fields in [ bonds ] line: '+line)
if fields[2] != '1':
raise ValueError('Unsupported function type in [ bonds ] line: '+line);
raise ValueError('Unsupported function type in [ bonds ] line: '+line)
self._currentMoleculeType.bonds.append(fields)
def _processAngle(self, line):
......@@ -310,9 +310,9 @@ class GromacsTopFile(object):
raise ValueError('Found [ angles ] section before [ moleculetype ]')
fields = line.split()
if len(fields) < 4:
raise ValueError('Too few fields in [ angles ] line: '+line);
raise ValueError('Too few fields in [ angles ] line: '+line)
if fields[3] not in ('1', '5'):
raise ValueError('Unsupported function type in [ angles ] line: '+line);
raise ValueError('Unsupported function type in [ angles ] line: '+line)
self._currentMoleculeType.angles.append(fields)
def _processDihedral(self, line):
......@@ -321,9 +321,9 @@ class GromacsTopFile(object):
raise ValueError('Found [ dihedrals ] section before [ moleculetype ]')
fields = line.split()
if len(fields) < 5:
raise ValueError('Too few fields in [ dihedrals ] line: '+line);
raise ValueError('Too few fields in [ dihedrals ] line: '+line)
if fields[4] not in ('1', '2', '3', '4', '9'):
raise ValueError('Unsupported function type in [ dihedrals ] line: '+line);
raise ValueError('Unsupported function type in [ dihedrals ] line: '+line)
self._currentMoleculeType.dihedrals.append(fields)
def _processExclusion(self, line):
......@@ -332,7 +332,7 @@ class GromacsTopFile(object):
raise ValueError('Found [ exclusions ] section before [ moleculetype ]')
fields = line.split()
if len(fields) < 2:
raise ValueError('Too few fields in [ exclusions ] line: '+line);
raise ValueError('Too few fields in [ exclusions ] line: '+line)
self._currentMoleculeType.exclusions.append(fields)
def _processPair(self, line):
......@@ -341,9 +341,9 @@ class GromacsTopFile(object):
raise ValueError('Found [ pairs ] section before [ moleculetype ]')
fields = line.split()
if len(fields) < 3:
raise ValueError('Too few fields in [ pairs ] line: '+line);
raise ValueError('Too few fields in [ pairs ] line: '+line)
if fields[2] != '1':
raise ValueError('Unsupported function type in [ pairs ] line: '+line);
raise ValueError('Unsupported function type in [ pairs ] line: '+line)
self._currentMoleculeType.pairs.append(fields)
def _processCmap(self, line):
......@@ -352,14 +352,14 @@ class GromacsTopFile(object):
raise ValueError('Found [ cmap ] section before [ moleculetype ]')
fields = line.split()
if len(fields) < 6:
raise ValueError('Too few fields in [ cmap ] line: '+line);
raise ValueError('Too few fields in [ cmap ] line: '+line)
self._currentMoleculeType.cmaps.append(fields)
def _processAtomType(self, line):
"""Process a line in the [ atomtypes ] category."""
fields = line.split()
if len(fields) < 6:
raise ValueError('Too few fields in [ atomtypes ] line: '+line);
raise ValueError('Too few fields in [ atomtypes ] line: '+line)
if len(fields[3]) == 1:
# Bonded type and atomic number are both missing.
fields.insert(1, None)
......@@ -377,27 +377,27 @@ class GromacsTopFile(object):
"""Process a line in the [ bondtypes ] category."""
fields = line.split()
if len(fields) < 5:
raise ValueError('Too few fields in [ bondtypes ] line: '+line);
raise ValueError('Too few fields in [ bondtypes ] line: '+line)
if fields[2] != '1':
raise ValueError('Unsupported function type in [ bondtypes ] line: '+line);
raise ValueError('Unsupported function type in [ bondtypes ] line: '+line)
self._bondTypes[tuple(fields[:2])] = fields
def _processAngleType(self, line):
"""Process a line in the [ angletypes ] category."""
fields = line.split()
if len(fields) < 6:
raise ValueError('Too few fields in [ angletypes ] line: '+line);
raise ValueError('Too few fields in [ angletypes ] line: '+line)
if fields[3] not in ('1', '5'):
raise ValueError('Unsupported function type in [ angletypes ] line: '+line);
raise ValueError('Unsupported function type in [ angletypes ] line: '+line)
self._angleTypes[tuple(fields[:3])] = fields
def _processDihedralType(self, line):
"""Process a line in the [ dihedraltypes ] category."""
fields = line.split()
if len(fields) < 7:
raise ValueError('Too few fields in [ dihedraltypes ] line: '+line);
raise ValueError('Too few fields in [ dihedraltypes ] line: '+line)
if fields[4] not in ('1', '2', '3', '4', '9'):
raise ValueError('Unsupported function type in [ dihedraltypes ] line: '+line);
raise ValueError('Unsupported function type in [ dihedraltypes ] line: '+line)
key = tuple(fields[:5])
if fields[4] == '9' and key in self._dihedralTypes:
# There are multiple dihedrals defined for these atom types.
......@@ -409,25 +409,25 @@ class GromacsTopFile(object):
"""Process a line in the [ implicit_genborn_params ] category."""
fields = line.split()
if len(fields) < 6:
raise ValueError('Too few fields in [ implicit_genborn_params ] line: '+line);
raise ValueError('Too few fields in [ implicit_genborn_params ] line: '+line)
self._implicitTypes[fields[0]] = fields
def _processPairType(self, line):
"""Process a line in the [ pairtypes ] category."""
fields = line.split()
if len(fields) < 5:
raise ValueError('Too few fields in [ pairtypes] line: '+line);
raise ValueError('Too few fields in [ pairtypes] line: '+line)
if fields[2] != '1':
raise ValueError('Unsupported function type in [ pairtypes ] line: '+line);
raise ValueError('Unsupported function type in [ pairtypes ] line: '+line)
self._pairTypes[tuple(fields[:2])] = fields
def _processCmapType(self, line):
"""Process a line in the [ cmaptypes ] category."""
fields = line.split()
if len(fields) < 8 or len(fields) < 8+int(fields[6])*int(fields[7]):
raise ValueError('Too few fields in [ cmaptypes ] line: '+line);
raise ValueError('Too few fields in [ cmaptypes ] line: '+line)
if fields[5] != '1':
raise ValueError('Unsupported function type in [ cmaptypes ] line: '+line);
raise ValueError('Unsupported function type in [ cmaptypes ] line: '+line)
self._cmapTypes[tuple(fields[:5])] = fields
def __init__(self, file, periodicBoxVectors=None, unitCellDimensions=None, includeDir=None, defines=None):
......
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @ 86d8dbf9
......@@ -34,8 +34,7 @@ DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
from __future__ import absolute_import
from __future__ import print_function
from __future__ import absolute_import, print_function
#=============================================================================================
# GLOBAL IMPORTS
......@@ -553,87 +552,6 @@ class PrmtopLoader(object):
self._excludedAtoms.append(atomList)
return self._excludedAtoms
def getGBParms(self, gbmodel, elements):
"""Return list giving GB params, Radius and screening factor"""
gb_List=[]
radii=[float(r) for r in self._raw_data["RADII"]]
screen=[float(s) for s in self._raw_data["SCREEN"]]
if gbmodel == 'GBn2':
alpha = [0 for i in self._raw_data['RADII']]
beta = [0 for i in self._raw_data['RADII']]
gamma = [0 for i in self._raw_data['RADII']]
# Update screening parameters for GBn if specified
if gbmodel == 'GBn':
if elements is None:
raise Exception('GBn model requires element information')
for i, element in enumerate(elements):
if element is elem.carbon:
screen[i] = 0.48435382330
elif element is elem.hydrogen:
screen[i] = 1.09085413633
elif element is elem.nitrogen:
screen[i] = 0.700147318409
elif element is elem.oxygen:
screen[i] = 1.06557401132
elif element is elem.sulfur:
screen[i] = 0.602256336067
else:
screen[i] = 0.5
# radii is currently in Angstroms right now. GBn lookup tables
# only support radii between 1.0 and 2.0
if radii[i] < 1.0 or radii[i] > 2.0:
raise ValueError('GBn requires intrinsic radii between 1 and '
'2 Angstroms (%.3f found for atom %d)' %
(radii[i], i))
if gbmodel == 'GBn2':
if elements is None:
raise Exception('GBn2 model requires element information')
for i, element in enumerate(elements):
if element is elem.carbon:
screen[i] = 1.058554
alpha[i] = 0.733756
beta[i] = 0.506378
gamma[i] = 0.205844
elif element is elem.hydrogen:
screen[i] = 1.425952
alpha[i] = 0.788440
beta[i] = 0.798699
gamma[i] = 0.437334
elif element is elem.nitrogen:
screen[i] = 0.733599
alpha[i] = 0.503364
beta[i] = 0.316828
gamma[i] = 0.192915
elif element is elem.oxygen:
screen[i] = 1.061039
alpha[i] = 0.867814
beta[i] = 0.876635
gamma[i] = 0.387882
elif element is elem.sulfur:
screen[i] = -0.703469
alpha[i] = 0.867814
beta[i] = 0.876635
gamma[i] = 0.387882
else: # not optimized
screen[i] = 0.5
alpha[i] = 1.0
beta[i] = 0.8
gamma[i] = 4.85
# radii is currently in Angstroms right now. GBn lookup tables
# only support radii between 1.0 and 2.0
if radii[i] < 1.0 or radii[i] > 2.0:
raise ValueError('GBn2 requires intrinsic radii between 1 and '
'2 Angstroms (%.3f found for atom %d)' %
(radii[i], i))
lengthConversionFactor = units.angstrom.conversion_factor_to(units.nanometer)
if gbmodel == 'GBn2':
for rad, scr, alp, bet, gam in zip(radii, screen, alpha, beta, gamma):
gb_List.append((rad*lengthConversionFactor, scr, alp, bet, gam))
else:
for rad, scr in zip(radii, screen):
gb_List.append((rad*lengthConversionFactor, scr))
return gb_List
def getBoxBetaAndDimensions(self):
"""Return periodic boundary box beta angle and dimensions"""
beta=float(self._raw_data["BOX_DIMENSIONS"][0])
......@@ -1053,7 +971,6 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
cutoff = nonbondedCutoff
if units.is_quantity(cutoff):
cutoff = cutoff.value_in_unit(units.nanometers)
gb_parms = prmtop.getGBParms(gbmodel, elements)
if gbmodel == 'HCT':
gb = customgb.GBSAHCTForce(solventDielectric, soluteDielectric, 'ACE', cutoff, implicitSolventKappa)
elif gbmodel == 'OBC1':
......@@ -1070,7 +987,29 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
elif gbmodel == 'GBn2':
gb = customgb.GBSAGBn2Force(solventDielectric, soluteDielectric, 'ACE', cutoff, implicitSolventKappa)
else:
raise Exception("Illegal value specified for implicit solvent model")
raise ValueError("Illegal value specified for implicit solvent model")
if isinstance(gb, mm.GBSAOBCForce):
# Built-in GBSAOBCForce does not have getStandardParameters, so use
# the one from the equivalent CustomGBForce
gb_parms = customgb.GBSAOBC2Force.getStandardParameters(topology)
else:
gb_parms = type(gb).getStandardParameters(topology)
# Replace radii and screen, but screen *only* gets replaced by the
# prmtop contents for HCT, OBC1, and OBC2. GBn and GBn2 both override
# the prmtop screen factors from LEaP in sander and pmemd
if gbmodel in ('HCT', 'OBC1', 'OBC2'):
screen = [float(s) for s in prmtop._raw_data['SCREEN']]
else:
screen = [gb_parm[1] for gb_parm in gb_parms]
radii = [float(r)/10 for r in prmtop._raw_data['RADII']]
warned = False
for i, (r, s) in enumerate(zip(radii, screen)):
if abs(r - gb_parms[i][0]) > 1e-4 or abs(s - gb_parms[i][1]) > 1e-4:
if not warned:
warnings.warn('Non-optimal GB parameters detected for GB '
'model %s' % gbmodel)
warned = True
gb_parms[i][0], gb_parms[i][1] = r, s
for charge, gb_parm in zip(charges, gb_parms):
if gbmodel == 'OBC2' and implicitSolventKappa == 0:
......
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ 86d8dbf9
......@@ -29,10 +29,11 @@ OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
from __future__ import division
from __future__ import absolute_import
from __future__ import division, absolute_import
from collections import defaultdict
import copy
from simtk.openmm.app import element as E
from simtk.openmm import CustomGBForce, Continuous2DFunction
import simtk.unit as u
......@@ -196,6 +197,141 @@ for i in range (len(d0)):
d0[i]=d0[i]/10
m0[i]=m0[i]*10
def _get_bonded_atom_list(topology):
""" Returns a list of atoms bonded to each other atom in a dict """
bondeds = defaultdict(list)
for a1, a2 in topology.bonds():
bondeds[a1].append(a2)
bondeds[a2].append(a1)
return bondeds
def _is_carboxylateO(atom, all_bonds):
if atom is not E.oxygen: return False
bondeds = all_bonds[atom]
if len(bondeds) != 1:
return False
if bondeds[0].element is not E.carbon:
return False
bondedsC = all_bonds[bondeds[0]]
if len(bondedsC) != 3:
return False
for a3 in bondedsC:
if a3 is atom: continue
if a3.element is E.oxygen:
break
else:
return False
# If we got here, must be a carboxylate
return True
def _bondi_radii(topology):
""" Sets the bondi radii """
radii = [0.0 for atom in topology.atoms()]
for i, atom in enumerate(topology.atoms()):
if atom.element is E.carbon:
radii[i] = 1.7
elif atom.element in (E.hydrogen, E.deuterium):
radii[i] = 1.2
elif atom.element is E.nitrogen:
radii[i] = 1.55
elif atom.element is E.oxygen:
radii[i] = 1.5
elif atom.element is E.fluorine:
radii[i] = 1.5
elif atom.element is E.silicon:
radii[i] = 2.1
elif atom.element is E.phosphorus:
radii[i] = 1.85
elif atom.element is E.sulfur:
radii[i] = 1.8
elif atom.element is E.chlorine:
radii[i] = 1.5
else:
radii[i] = 1.5
return radii # converted to nanometers above
def _mbondi_radii(topology):
""" Sets the mbondi radii """
radii = [0.0 for atom in topology.atoms()]
all_bonds = _get_bonded_atom_list(topology)
for i, atom in enumerate(topology.atoms()):
# Radius of H atom depends on element it is bonded to
if atom.element in (E.hydrogen, E.deuterium):
bondeds = all_bonds[atom]
if bondeds[0].element in (E.carbon, E.nitrogen):
radii[i] = 1.3
elif bondeds[0].type.atomic_number in (E.oxygen, E.sulfur):
radii[i] = 0.8
else:
radii[i] = 1.2
# Radius of C atom depends on what type it is
elif atom.element is E.carbon:
radii[i] = 1.7
# All other elements have fixed radii for all types/partners
elif atom.element is E.nitrogen:
radii[i] = 1.55
elif atom.element is E.oxygen:
radii[i] = 1.5
elif atom.element is E.fluorine:
radii[i] = 1.5
elif atom.element is E.silicon:
radii[i] = 2.1
elif atom.element is E.phosphorus:
radii[i] = 1.85
elif atom.element is E.sulfur:
radii[i] = 1.8
elif atom.element is E.chlorine:
radii[i] = 1.5
else:
radii[i] = 1.5
return radii # converted to nanometers above
def _mbondi2_radii(topology):
""" Sets the mbondi2 radii """
radii = [0.0 for atom in topology.atoms()]
all_bonds = _get_bonded_atom_list(topology)
for i, atom in enumerate(topology.atoms()):
# Radius of H atom depends on element it is bonded to
if atom.element in (E.hydrogen, E.deuterium):
bondeds = all_bonds[atom]
if bondeds[0].element is E.nitrogen:
radii[i] = 1.3
else:
radii[i] = 1.2
# Radius of C atom depends on what type it is
elif atom.element is E.carbon:
radii[i] = 1.7
# All other elements have fixed radii for all types/partners
elif atom.element is E.nitrogen:
radii[i] = 1.55
elif atom.element is E.oxygen:
radii[i] = 1.5
elif atom.element is E.fluorine:
radii[i] = 1.5
elif atom.element is E.silicon:
radii[i] = 2.1
elif atom.element == E.phosphorus:
radii[i] = 1.85
elif atom.element == E.sulfur:
radii[i] = 1.8
elif atom.element == E.chlorine:
radii[i] = 1.5
else:
radii[i] = 1.5
return radii # Converted to nanometers above
def _mbondi3_radii(topology):
""" Sets the mbondi3 radii """
radii = _mbondi2_radii(topology)
all_bonds = _get_bonded_atom_list(topology)
for i, atom in enumerate(topology.atoms()):
# carboxylate and HH/HE (ARG)
if _is_carboxylateO(atom, all_bonds):
radii[i] = 1.4
elif atom.residue.name == 'ARG':
if atom.name.startswith('HH') or atom.name.startswith('HE'):
radii[i] = 1.17
return radii # Converted to nanometers above
def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, kappa, offset):
# Add the energy terms to the CustomGBForce. These are identical for all the GB models.
......@@ -231,6 +367,22 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k
force.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*(1/f-"+str(1/cutoff)+");"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions)
_SCREEN_PARAMETERS = { # normal, GBn, GBn2
E.hydrogen : (0.85, 1.09085413633, 1.425952),
E.carbon : (0.72, 0.48435382330, 1.058554),
E.nitrogen : (0.79, 0.700147318409, 0.733599),
E.oxygen : (0.85, 1.06557401132, 1.061039),
E.fluorine : (0.88, 0.5, 0.5),
E.phosphorus : (0.86, 0.5, 0.5),
E.sulfur : (0.96, 0.602256336067, -0.703469),
None : (0.8, 0.5, 0.5) # default
}
_SCREEN_PARAMETERS[E.deuterium] = _SCREEN_PARAMETERS[E.hydrogen]
def _screen_parameter(atom):
if atom.element in _SCREEN_PARAMETERS:
return _SCREEN_PARAMETERS[atom.element]
return _SCREEN_PARAMETERS[None]
class CustomAmberGBForce(CustomGBForce):
OFFSET = 0.009
......@@ -254,6 +406,24 @@ class CustomAmberGBForce(CustomGBForce):
CustomGBForce.addParticle(self, params)
return params
@staticmethod
def getStandardParameters(topology):
""" Gets list of standard parameters for this GB model based on an input Topology
Parameters
----------
topology : simtk.openmm.app.Topology
Topology of the system to get parameters for
Returns
-------
list of float
List of all parameters needed for this GB model. These can be passed
to addParticle or setParticleParameters after the charge is inserted
at the beginning of the list
"""
raise NotImplementedError('Must override getStandardParameters in subclasses')
"""
Amber Equivalent: igb = 1
"""
......@@ -275,6 +445,13 @@ class GBSAHCTForce(CustomAmberGBForce):
self.addComputedValue("B", "1/(1/or-I)", CustomGBForce.SingleParticle)
_createEnergyTerms(self, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
@staticmethod
def getStandardParameters(topology):
radii = [[x/10] for x in _mbondi_radii(topology)]
for i, atom in enumerate(topology.atoms()):
radii[i].append(_screen_parameter(atom)[0])
return radii
"""
Amber Equivalents: igb = 2
"""
......@@ -297,10 +474,17 @@ class GBSAOBC1Force(CustomAmberGBForce):
"psi=I*or; radius=or+offset; offset=0.009", CustomGBForce.SingleParticle)
_createEnergyTerms(self, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.009)
@staticmethod
def getStandardParameters(topology):
radii = [[x/10] for x in _mbondi2_radii(topology)]
for i, atom in enumerate(topology.atoms()):
radii[i].append(_screen_parameter(atom)[0])
return radii
"""
Amber Equivalents: igb = 5
"""
class GBSAOBC2Force(CustomAmberGBForce):
class GBSAOBC2Force(GBSAOBC1Force):
def __init__(self, solventDielectric=78.5, soluteDielectric=1, SA=None,
cutoff=None, kappa=0.0):
......@@ -359,6 +543,13 @@ class GBSAGBnForce(CustomAmberGBForce):
if parameters[1] < 0.1 or parameters[1] > 0.2:
raise ValueError('Radii must be between 1 and 2 Angstroms for neck lookup')
@staticmethod
def getStandardParameters(topology):
radii = [[x/10] for x in _bondi_radii(topology)]
for i, atom in enumerate(topology.atoms()):
radii[i].append(_screen_parameter(atom)[1])
return radii
"""
Amber Equivalents: igb = 8
"""
......@@ -393,3 +584,22 @@ class GBSAGBn2Force(GBSAGBnForce):
self.addComputedValue("B", "1/(1/or-tanh(alpha*psi-beta*psi^2+gamma*psi^3)/radius);"
"psi=I*or; radius=or+offset; offset=0.0195141", CustomGBForce.SingleParticle)
_createEnergyTerms(self, solventDielectric, soluteDielectric, SA, cutoff, kappa, 0.0195141)
@staticmethod
def getStandardParameters(topology):
radii = [[x/10] for x in _mbondi3_radii(topology)]
for i, atom in enumerate(topology.atoms()):
radii[i].append(_screen_parameter(atom)[2])
if atom.element in (E.hydrogen, E.deuterium):
radii[i].extend([0.788440, 0.798699, 0.437334])
elif atom.element is E.carbon:
radii[i].extend([0.733756, 0.506378, 0.205844])
elif atom.element is E.nitrogen:
radii[i].extend([0.503364, 0.316828, 0.192915])
elif atom.element is E.oxygen:
radii[i].extend([0.867814, 0.876635, 0.387882])
elif atom.element is E.sulfur:
radii[i].extend([0.867814, 0.876635, 0.387882])
else:
radii[i].extend([0.8, 4.85, 0.5])
return radii
wrappers/python/simtk/openmm/app/modeller.py
View file @ 86d8dbf9
......@@ -264,7 +264,7 @@ class Modeller(object):
2. Water molecules are removed if their distance to any solute atom is less than the sum of their van der Waals radii.
3. If the solute is charged and neutralize=True, enough positive or negative ions are added to neutralize it. Each ion is added by
randomly selecting a water molecule and replacing it with the ion.
4. Ion pairs are added to give the requested total ionic strength.
4. Ion pairs are added to give the requested total ionic strength. Note that only monovalent ions are currently supported.
The box size can be specified in any of several ways:
......@@ -298,6 +298,7 @@ class Modeller(object):
ionicStrength : concentration=0*molar
the total concentration of ions (both positive and negative) to add. This
does not include ions that are added to neutralize the system.
Note that only monovalent ions are currently supported.
neutralize : bool=True
whether to add ions to neutralize the system
"""
......@@ -522,7 +523,7 @@ class Modeller(object):
# Add ions based on the desired ionic strength.
numIons = len(addedWaters)*ionicStrength/(55.4*molar) # Pure water is about 55.4 molar (depending on temperature)
numPairs = int(floor(numIons/2+0.5))
numPairs = int(floor(numIons+0.5))
for i in range(numPairs):
addIon(positiveElement)
for i in range(numPairs):
......@@ -1103,7 +1104,7 @@ class Modeller(object):
else:
a2 = newAtoms[matchingAtoms[atom2]]
newTopology.addBond(a1, a2)
for bond in self.topology.bonds():
if bond[0] in newAtoms and bond[1] in newAtoms:
newTopology.addBond(newAtoms[bond[0]], newAtoms[bond[1]])
......@@ -1135,6 +1136,6 @@ class Modeller(object):
delta *= (distance-length)/length
newPositions[atom1] -= weights[0]*delta
newPositions[atom2] += weights[1]*delta
self.topology = newTopology
self.positions = newPositions
wrappers/python/simtk/openmm/app/topology.py
View file @ 86d8dbf9
......@@ -71,20 +71,17 @@ class Topology(object):
def getNumAtoms(self):
"""Return the number of atoms in the Topology.
"""
natom = self._numAtoms
return natom
return self._numAtoms
def getNumResidues(self):
"""Return the number of residues in the Topology.
"""
nres = self._numResidues
return nres
return self._numResidues
def getNumChains(self):
"""Return the number of chains in the Topology.
"""
nchain = len(self._chains)
return nchain
return len(self._chains)
def addChain(self, id=None):
"""Create a new Chain and add it to the Topology.
......
wrappers/python/tests/TestModeller.py
View file @ 86d8dbf9
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