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Unverified Commit 7ada5dd0 authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #2274 from JoaoRodrigues/ion_fix 

Improved ion addition to both addSolvent() and addMembrane()
parents 0ee983bc 6b6f92a0
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Showing with 166 additions and 83 deletions
wrappers/python/simtk/openmm/app/modeller.py
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......@@ -46,6 +46,7 @@ from . import element as elem
import gc
import os
import random
import sys
import xml.etree.ElementTree as etree
from copy import deepcopy
from math import ceil, floor
......@@ -257,6 +258,120 @@ class Modeller(object):
self.topology = newTopology
self.positions = newPositions
def _addIons(self, forcefield, replaceableMols, ionCutoff=0.05*nanometer, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar, neutralize=True):
"""Adds ions to the system by replacing certain molecules.
Parameters
----------
forcefield : ForceField
the ForceField to use to determine the total charge of the system.
replaceableMols : dict
the molecules to replace by ions, as a dictionary of residue:positions
ionCutoff: distance=0.5*nanometer
positiveIon : string='Na+'
the type of positive ion to add. Allowed values are 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'
negativeIon : string='Cl-'
the type of negative ion to add. Allowed values are 'Cl-', 'Br-', 'F-', and 'I-'. Be aware
that not all force fields support all ion types.
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
"""
posIonElements = {'Cs+': elem.cesium, 'K+': elem.potassium,
'Li+': elem.lithium, 'Na+': elem.sodium,
'Rb+': elem.rubidium}
negIonElements = {'Cl-': elem.chlorine, 'Br-': elem.bromine,
'F-': elem.fluorine, 'I-': elem.iodine}
ionPositions = []
numReplaceableMols = len(replaceableMols)
# Fetch ion elements from user input
if positiveIon not in posIonElements:
raise ValueError('Illegal value for positive ion: {}'.format(positiveIon))
if negativeIon not in negIonElements:
raise ValueError('Illegal value for negative ion: {}'.format(negativeIon))
positiveElement = posIonElements[positiveIon]
negativeElement = negIonElements[negativeIon]
# Determine the total charge of the system
system = forcefield.createSystem(self.topology)
for i in range(system.getNumForces()):
if isinstance(system.getForce(i), NonbondedForce):
nonbonded = system.getForce(i)
break
else:
raise ValueError('The ForceField does not specify a NonbondedForce')
totalCharge = 0.0
for i in range(nonbonded.getNumParticles()):
nb_i = nonbonded.getParticleParameters(i)
totalCharge += nb_i[0].value_in_unit(elementary_charge)
# Round to nearest integer
totalCharge = int(floor(0.5 + totalCharge))
# Figure out how many ions to add based on requested params/concentration
numPositive, numNegative = 0, 0
if neutralize:
if abs(totalCharge) > numReplaceableMols:
raise Exception('Cannot neutralize the system because the charge is greater than the number of available positions for ions')
if totalCharge > 0:
numNegative += totalCharge
else:
numPositive -= totalCharge
if ionicStrength > 0 * molar:
numIons = (numReplaceableMols - numPositive - numNegative) * ionicStrength / (55.4 * molar) # Pure water is about 55.4 molar (depending on temperature)
numPairs = int(floor(numIons + 0.5))
numPositive += numPairs
numNegative += numPairs
totalIons = numPositive + numNegative
# Randomly select a set of waters
# while ensuring ions are not placed too close to each other.
modeller = Modeller(self.topology, self.positions)
replaceableList = list(replaceableMols.keys())
numAddedIons = 0
numTrials = 10 # Attempts to add ions N times before quitting
toReplace = [] # list of molecules to be replaced
while numAddedIons < totalIons:
pickedMol = random.choice(replaceableList)
replaceableList.remove(pickedMol)
# Check distance to other ions
for pos in ionPositions:
distance = norm(pos - replaceableMols[pickedMol])
if distance <= ionCutoff:
numTrials -= 1
break
else:
toReplace.append(pickedMol)
ionPositions.append(replaceableMols[pickedMol])
numAddedIons += 1
n_trials = 10
if n_trials == 0:
raise ValueError('Could not add more than {} ions to the system'.format(numAddedIons))
# Replace waters/ions in the topology
modeller.delete(toReplace)
ionChain = modeller.topology.addChain()
for i, water in enumerate(toReplace):
element = (positiveElement if i < numPositive else negativeElement)
newResidue = modeller.topology.addResidue(element.symbol.upper(), ionChain)
modeller.topology.addAtom(element.symbol, element, newResidue)
modeller.positions.append(replaceableMols[water])
# Update topology/positions
self.topology = modeller.topology
self.positions = modeller.positions
def addSolvent(self, forcefield, model='tip3p', boxSize=None, boxVectors=None, padding=None, numAdded=None, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar, neutralize=True):
"""Add solvent (both water and ions) to the model to fill a rectangular box.
......@@ -361,17 +476,6 @@ class Modeller(object):
raise ValueError('Neither the box size, box vectors, nor padding was specified, and the Topology does not define unit cell dimensions')
invBox = Vec3(1.0/box[0], 1.0/box[1], 1.0/box[2])
# Identify the ion types.
posIonElements = {'Cs+':elem.cesium, 'K+':elem.potassium, 'Li+':elem.lithium, 'Na+':elem.sodium, 'Rb+':elem.rubidium}
negIonElements = {'Cl-':elem.chlorine, 'Br-':elem.bromine, 'F-':elem.fluorine, 'I-':elem.iodine}
if positiveIon not in posIonElements:
raise ValueError('Illegal value for positive ion: %s' % positiveIon)
if negativeIon not in negIonElements:
raise ValueError('Illegal value for negative ion: %s' % negativeIon)
positiveElement = posIonElements[positiveIon]
negativeElement = negIonElements[negativeIon]
# Have the ForceField build a System for the solute from which we can determine van der Waals radii.
system = forcefield.createSystem(self.topology)
......@@ -487,31 +591,6 @@ class Modeller(object):
filteredWaters.append(entry)
addedWaters = filteredWaters
# Add ions to neutralize the system.
def addIon(element):
# Replace a water by an ion.
index = random.randint(0, len(addedWaters)-1)
newResidue = newTopology.addResidue(element.symbol.upper(), newChain)
newTopology.addAtom(element.symbol, element, newResidue)
newPositions.append(addedWaters[index][1]*nanometer)
del addedWaters[index]
if neutralize:
totalCharge = int(floor(0.5+sum((nonbonded.getParticleParameters(i)[0].value_in_unit(elementary_charge) for i in range(system.getNumParticles())))))
if abs(totalCharge) > len(addedWaters):
raise Exception('Cannot neutralize the system because the charge is greater than the number of available positions for ions')
for i in range(abs(totalCharge)):
addIon(positiveElement if totalCharge < 0 else negativeElement)
# 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+0.5))
for i in range(numPairs):
addIon(positiveElement)
for i in range(numPairs):
addIon(negativeElement)
# Add the water molecules.
for index, pos in addedWaters:
......@@ -528,9 +607,23 @@ class Modeller(object):
for atom2 in molAtoms:
if atom2.element == elem.hydrogen:
newTopology.addBond(atom1, atom2)
self.topology = newTopology
self.positions = newPositions
# Convert water list to dictionary (residue:position)
waterPos = {}
_oxygen = elem.oxygen
for chain in newTopology.chains():
for residue in chain.residues():
if residue.name == 'HOH':
for atom in residue.atoms():
if atom.element == _oxygen:
waterPos[residue] = newPositions[atom.index]
# Add ions to neutralize the system.
self._addIons(forcefield, waterPos, positiveIon=positiveIon, negativeIon=negativeIon, ionicStrength=ionicStrength, neutralize=neutralize)
class _ResidueData:
"""Inner class used to encapsulate data about the hydrogens for a residue."""
def __init__(self, name):
......@@ -1206,17 +1299,6 @@ class Modeller(object):
nx = int(ceil((proteinSize[0]+2*minimumPadding)/patchSize[0]))
ny = int(ceil((proteinSize[1]+2*minimumPadding)/patchSize[1]))
# Identify the ion types.
posIonElements = {'Cs+':elem.cesium, 'K+':elem.potassium, 'Li+':elem.lithium, 'Na+':elem.sodium, 'Rb+':elem.rubidium}
negIonElements = {'Cl-':elem.chlorine, 'Br-':elem.bromine, 'F-':elem.fluorine, 'I-':elem.iodine}
if positiveIon not in posIonElements:
raise ValueError('Illegal value for positive ion: %s' % positiveIon)
if negativeIon not in negIonElements:
raise ValueError('Illegal value for negative ion: %s' % negativeIon)
positiveElement = posIonElements[positiveIon]
negativeElement = negIonElements[negativeIon]
# Record the bonds for each residue.
resBonds = defaultdict(list)
......@@ -1425,7 +1507,6 @@ class Modeller(object):
# We may have added extra water molecules inside the membrane. We really only wanted to extend the box
# without adding more water in the existing box, so remove the unwanted ones.
if needExtraWater:
toDelete = []
addedChain = list(modeller.topology.chains())[-1]
......@@ -1439,41 +1520,43 @@ class Modeller(object):
if len(toDelete) > 0:
modeller.delete(toDelete)
# Determine how many positive and negative ions to add.
numPositive = 0
numNegative = 0
if neutralize:
totalCharge = int(floor(0.5+sum((nonbonded.getParticleParameters(i)[0].value_in_unit(elementary_charge) for i in range(nonbonded.getNumParticles())))))
if abs(totalCharge) > len(waterPos):
raise Exception('Cannot neutralize the system because the charge is greater than the number of available positions for ions')
if totalCharge > 0:
numNegative += totalCharge
else:
numPositive -= totalCharge
if ionicStrength > 0*molar:
numIons = (len(waterPos)-numPositive-numNegative)*ionicStrength/(55.4*molar) # Pure water is about 55.4 molar (depending on temperature)
numPairs = int(floor(numIons+0.5))
numPositive += numPairs
numNegative += numPairs
totalIons = numPositive+numNegative
# Now add the ions. We do this by randomly selecting a set of waters that were just added and replacing
# them with ions.
if totalIons > 0:
toReplace = random.sample(list(waterPos), totalIons)
modeller.delete(toReplace)
ionChain = modeller.topology.addChain()
for i, water in enumerate(toReplace):
element = (positiveElement if i < numPositive else negativeElement)
newResidue = modeller.topology.addResidue(element.symbol.upper(), ionChain)
modeller.topology.addAtom(element.symbol, element, newResidue)
modeller.positions.append(waterPos[water]*nanometer)
self.topology = modeller.topology
self.positions = modeller.positions
# Select a subset of water molecules to replace with ions, ignoring
# those within a certain distance from either leaflet of the membrane.
waterPos = {} # redo because modeller.delete changes chain indexes
for chain in list(modeller.topology.chains())[-2:]:
for residue in chain.residues():
if residue.name == 'HOH':
for atom in residue.atoms():
if atom.element == elem.oxygen:
waterPos[residue] = modeller.positions[atom.index]
# Calculate lipid Z boundaries
lipidNames = {res.name for res in patch.topology.residues() if res.name != 'HOH'}
lipidZMax = sys.float_info.min
lipidZMin = sys.float_info.max
for res in modeller.topology.residues():
if res.name in lipidNames:
for atom in res.atoms():
atomZ = modeller.positions[atom.index][2].value_in_unit(nanometer)
lipidZMax = max(lipidZMax, atomZ)
lipidZMin = min(lipidZMin, atomZ)
# Ignore waters that are within a certain distance of the membrane
lipidOffset = 0.25
upperZBoundary = (lipidZMax + lipidOffset)
lowerZBoundary = (lipidZMin - lipidOffset)
waterResidues = list(waterPos)
for wRes in waterResidues:
waterZ = waterPos[wRes][2]
if lowerZBoundary < waterZ.value_in_unit(nanometer) < upperZBoundary:
del waterPos[wRes]
self._addIons(forcefield, waterPos, positiveIon=positiveIon, negativeIon=negativeIon, ionicStrength=ionicStrength, neutralize=neutralize)
class _CellList(object):
"""This class organizes atom positions into cells, so the neighbors of a point can be quickly retrieved"""
......
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