def test_Disulfides(self):
"""Test that various force fields handle disulfides correctly."""
pdb = PDBFile('systems/bpti.pdb')
for ff in [
'amber99sb.xml', 'amber14-all.xml', 'charmm36.xml',
'amberfb15.xml', 'amoeba2013.xml'
]:
forcefield = ForceField(ff)
system = forcefield.createSystem(pdb.topology)
def test_Forces(self):
"""Compute forces and compare them to ones generated with a previous version of OpenMM to ensure they haven't changed."""
pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
forcefield = ForceField('amoeba2013.xml', 'amoeba2013_gk.xml')
system = forcefield.createSystem(pdb.topology, polarization='direct')
integrator = VerletIntegrator(0.001)
context = Context(system, integrator)
context.setPositions(pdb.positions)
state1 = context.getState(getForces=True)
with open('systems/alanine-dipeptide-amoeba-forces.xml') as input:
state2 = XmlSerializer.deserialize(input.read())
for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
diff = norm(f1-f2)
self.assertTrue(diff < 0.1 or diff/norm(f1) < 1e-3)
def test_Forces(self):
"""Compute forces and compare them to ones generated with a previous version of OpenMM to ensure they haven't changed."""
pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
forcefield = ForceField('amoeba2013.xml', 'amoeba2013_gk.xml')
system = forcefield.createSystem(pdb.topology, polarization='direct')
integrator = VerletIntegrator(0.001)
context = Context(system, integrator)
context.setPositions(pdb.positions)
state1 = context.getState(getForces=True)
with open('systems/alanine-dipeptide-amoeba-forces.xml') as input:
state2 = XmlSerializer.deserialize(input.read())
for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
diff = norm(f1-f2)
self.assertTrue(diff < 0.1 or diff/norm(f1) < 1e-3)
def _create_system(self):
"""
Create the OpenMM System object.
"""
# Create file-like objects from ffxml contents because ForceField cannot yet read strings.
from StringIO import StringIO
ffxml_streams = list()
for ffxml in self._ffxmls:
ffxml_streams.append(StringIO(ffxml))
# Create ForceField.
forcefield = app.ForceField(ffxml_streams)
# Create System from topology.
self._system = forcefield.createSystem(self._topology, **self.system_creation_parameters)
return
def _create_system(self):
"""
Create the OpenMM System object.
"""
# Create file-like objects from ffxml contents because ForceField cannot yet read strings.
from StringIO import StringIO
ffxml_streams = list()
for ffxml in self._ffxmls:
ffxml_streams.append(StringIO(ffxml))
# Create ForceField.
forcefield = app.ForceField(*ffxml_streams)
# Create System from topology.
self._system = forcefield.createSystem(self._topology, **self.system_creation_parameters)
return
def test_ggenerateTemplatesForUnmatchedResidues(self):
"""Test generation of blank forcefield residue templates for unmatched residues."""
#
# Test where we generate parameters for only a ligand.
#
# Load the PDB file.
pdb = PDBFile(os.path.join('systems', 'nacl-water.pdb'))
# Create a ForceField object.
forcefield = ForceField('tip3p.xml')
# Get list of unmatched residues.
unmatched_residues = forcefield.getUnmatchedResidues(pdb.topology)
[templates, residues] = forcefield.generateTemplatesForUnmatchedResidues(pdb.topology)
# Check results.
self.assertEqual(len(unmatched_residues), 24)
self.assertEqual(len(residues), 2)
self.assertEqual(len(templates), 2)
unique_names = set([ residue.name for residue in residues ])
self.assertTrue('HOH' not in unique_names)
self.assertTrue('NA' in unique_names)
self.assertTrue('CL' in unique_names)
template_names = set([ template.name for template in templates ])
self.assertTrue('HOH' not in template_names)
self.assertTrue('NA' in template_names)
self.assertTrue('CL' in template_names)
# Define forcefield parameters using returned templates.
# NOTE: This parameter definition file will currently only work for residues that either have
# no external bonds or external bonds to other residues parameterized by the simpleTemplateGenerator.
simple_ffxml_contents = """
<ForceField>
<AtomTypes>
<Type name="XXX" class="XXX" element="C" mass="12.0"/>
</AtomTypes>
<HarmonicBondForce>
<Bond type1="XXX" type2="XXX" length="0.1409" k="392459.2"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="XXX" type2="XXX" type3="XXX" angle="2.09439510239" k="527.184"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
<Atom type="XXX" charge="0.000" sigma="0.315" epsilon="0.635"/>
</NonbondedForce>
</ForceField>"""
#
# Test the pre-geenration of missing residue template for a ligand.
#
# Load the PDB file.
pdb = PDBFile(os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
# Create a ForceField object.
forcefield = ForceField('amber99sb.xml', 'tip3p.xml', StringIO(simple_ffxml_contents))
# Get list of unique unmatched residues.
[templates, residues] = forcefield.generateTemplatesForUnmatchedResidues(pdb.topology)
# Add residue templates to forcefield.
for template in templates:
# Replace atom types.
for atom in template.atoms:
atom.type = 'XXX'
# Register the template.
forcefield.registerResidueTemplate(template)
# Parameterize system.
system = forcefield.createSystem(pdb.topology, nonbondedMethod=NoCutoff)
def test_residueTemplateGenerator(self):
"""Test the ability to add residue template generators to parameterize unmatched residues."""
def simpleTemplateGenerator(forcefield, residue):
"""\
Simple residue template generator.
This implementation uses the programmatic API to define residue templates.
NOTE: We presume we have already loaded the force definitions into ForceField.
"""
# Generate a unique prefix name for generating parameters.
from uuid import uuid4
template_name = uuid4()
# Create residue template.
from simtk.openmm.app.forcefield import _createResidueTemplate
template = _createResidueTemplate(residue) # use helper function
template.name = template_name # replace template name
for (template_atom, residue_atom) in zip(template.atoms, residue.atoms()):
template_atom.type = 'XXX' # replace atom type
# Register the template.
forcefield.registerResidueTemplate(template)
# Signal that we have successfully parameterized the residue.
return True
# Define forcefield parameters used by simpleTemplateGenerator.
# NOTE: This parameter definition file will currently only work for residues that either have
# no external bonds or external bonds to other residues parameterized by the simpleTemplateGenerator.
simple_ffxml_contents = """
<ForceField>
<AtomTypes>
<Type name="XXX" class="XXX" element="C" mass="12.0"/>
</AtomTypes>
<HarmonicBondForce>
<Bond type1="XXX" type2="XXX" length="0.1409" k="392459.2"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="XXX" type2="XXX" type3="XXX" angle="2.09439510239" k="527.184"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
<Atom type="XXX" charge="0.000" sigma="0.315" epsilon="0.635"/>
</NonbondedForce>
</ForceField>"""
#
# Test where we generate parameters for only a ligand.
#
# Load the PDB file.
pdb = PDBFile(os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
# Create a ForceField object.
forcefield = ForceField('amber99sb.xml', 'tip3p.xml', StringIO(simple_ffxml_contents))
# Add the residue template generator.
forcefield.registerTemplateGenerator(simpleTemplateGenerator)
# Parameterize system.
system = forcefield.createSystem(pdb.topology, nonbondedMethod=NoCutoff)
# TODO: Test energies are finite?
#
# Test for a few systems where we generate all parameters.
#
tests = [
{ 'pdb_filename' : 'alanine-dipeptide-implicit.pdb', 'nonbondedMethod' : NoCutoff },
{ 'pdb_filename' : 'lysozyme-implicit.pdb', 'nonbondedMethod' : NoCutoff },
{ 'pdb_filename' : 'alanine-dipeptide-explicit.pdb', 'nonbondedMethod' : CutoffPeriodic },
]
# Test all systems with separate ForceField objects.
for test in tests:
# Load the PDB file.
pdb = PDBFile(os.path.join('systems', test['pdb_filename']))
# Create a ForceField object.
forcefield = ForceField(StringIO(simple_ffxml_contents))
# Add the residue template generator.
forcefield.registerTemplateGenerator(simpleTemplateGenerator)
# Parameterize system.
system = forcefield.createSystem(pdb.topology, nonbondedMethod=test['nonbondedMethod'])
# TODO: Test energies are finite?
# Now test all systems with a single ForceField object.
# Create a ForceField object.
forcefield = ForceField(StringIO(simple_ffxml_contents))
# Add the residue template generator.
forcefield.registerTemplateGenerator(simpleTemplateGenerator)
for test in tests:
# Load the PDB file.
pdb = PDBFile(os.path.join('systems', test['pdb_filename']))
# Parameterize system.
system = forcefield.createSystem(pdb.topology, nonbondedMethod=test['nonbondedMethod'])
def test_ggenerateTemplatesForUnmatchedResidues(self):
"""Test generation of blank forcefield residue templates for unmatched residues."""
#
# Test where we generate parameters for only a ligand.
#
# Load the PDB file.
pdb = PDBFile(os.path.join('systems', 'nacl-water.pdb'))
# Create a ForceField object.
forcefield = ForceField('tip3p.xml')
# Get list of unmatched residues.
unmatched_residues = forcefield.getUnmatchedResidues(pdb.topology)
[templates, residues
] = forcefield.generateTemplatesForUnmatchedResidues(pdb.topology)
# Check results.
self.assertEqual(len(unmatched_residues), 24)
self.assertEqual(len(residues), 2)
self.assertEqual(len(templates), 2)
unique_names = set([residue.name for residue in residues])
self.assertTrue('HOH' not in unique_names)
self.assertTrue('NA' in unique_names)
self.assertTrue('CL' in unique_names)
template_names = set([template.name for template in templates])
self.assertTrue('HOH' not in template_names)
self.assertTrue('NA' in template_names)
self.assertTrue('CL' in template_names)
# Define forcefield parameters using returned templates.
# NOTE: This parameter definition file will currently only work for residues that either have
# no external bonds or external bonds to other residues parameterized by the simpleTemplateGenerator.
simple_ffxml_contents = """
<ForceField>
<AtomTypes>
<Type name="XXX" class="XXX" element="C" mass="12.0"/>
</AtomTypes>
<HarmonicBondForce>
<Bond type1="XXX" type2="XXX" length="0.1409" k="392459.2"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="XXX" type2="XXX" type3="XXX" angle="2.09439510239" k="527.184"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
<Atom type="XXX" charge="0.000" sigma="0.315" epsilon="0.635"/>
</NonbondedForce>
</ForceField>"""
#
# Test the pre-geenration of missing residue template for a ligand.
#
# Load the PDB file.
pdb = PDBFile(
os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
# Create a ForceField object.
forcefield = ForceField('amber99sb.xml', 'tip3p.xml',
StringIO(simple_ffxml_contents))
# Get list of unique unmatched residues.
[templates, residues
] = forcefield.generateTemplatesForUnmatchedResidues(pdb.topology)
# Add residue templates to forcefield.
for template in templates:
# Replace atom types.
for atom in template.atoms:
atom.type = 'XXX'
# Register the template.
forcefield.registerResidueTemplate(template)
# Parameterize system.
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=NoCutoff)
def test_residueTemplateGenerator(self):
"""Test the ability to add residue template generators to parameterize unmatched residues."""
def simpleTemplateGenerator(forcefield, residue):
"""\
Simple residue template generator.
This implementation uses the programmatic API to define residue templates.
NOTE: We presume we have already loaded the force definitions into ForceField.
"""
# Generate a unique prefix name for generating parameters.
from uuid import uuid4
template_name = uuid4()
# Create residue template.
from simtk.openmm.app.forcefield import _createResidueTemplate
template = _createResidueTemplate(residue) # use helper function
template.name = template_name # replace template name
for (template_atom, residue_atom) in zip(template.atoms,
residue.atoms()):
template_atom.type = 'XXX' # replace atom type
# Register the template.
forcefield.registerResidueTemplate(template)
# Signal that we have successfully parameterized the residue.
return True
# Define forcefield parameters used by simpleTemplateGenerator.
# NOTE: This parameter definition file will currently only work for residues that either have
# no external bonds or external bonds to other residues parameterized by the simpleTemplateGenerator.
simple_ffxml_contents = """
<ForceField>
<AtomTypes>
<Type name="XXX" class="XXX" element="C" mass="12.0"/>
</AtomTypes>
<HarmonicBondForce>
<Bond type1="XXX" type2="XXX" length="0.1409" k="392459.2"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="XXX" type2="XXX" type3="XXX" angle="2.09439510239" k="527.184"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
<Atom type="XXX" charge="0.000" sigma="0.315" epsilon="0.635"/>
</NonbondedForce>
</ForceField>"""
#
# Test where we generate parameters for only a ligand.
#
# Load the PDB file.
pdb = PDBFile(
os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
# Create a ForceField object.
forcefield = ForceField('amber99sb.xml', 'tip3p.xml',
StringIO(simple_ffxml_contents))
# Add the residue template generator.
forcefield.registerTemplateGenerator(simpleTemplateGenerator)
# Parameterize system.
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=NoCutoff)
# TODO: Test energies are finite?
#
# Test for a few systems where we generate all parameters.
#
tests = [
{
'pdb_filename': 'alanine-dipeptide-implicit.pdb',
'nonbondedMethod': NoCutoff
},
{
'pdb_filename': 'lysozyme-implicit.pdb',
'nonbondedMethod': NoCutoff
},
{
'pdb_filename': 'alanine-dipeptide-explicit.pdb',
'nonbondedMethod': CutoffPeriodic
},
]
# Test all systems with separate ForceField objects.
for test in tests:
# Load the PDB file.
pdb = PDBFile(os.path.join('systems', test['pdb_filename']))
# Create a ForceField object.
forcefield = ForceField(StringIO(simple_ffxml_contents))
# Add the residue template generator.
forcefield.registerTemplateGenerator(simpleTemplateGenerator)
# Parameterize system.
system = forcefield.createSystem(
pdb.topology, nonbondedMethod=test['nonbondedMethod'])
# TODO: Test energies are finite?
# Now test all systems with a single ForceField object.
# Create a ForceField object.
forcefield = ForceField(StringIO(simple_ffxml_contents))
# Add the residue template generator.
forcefield.registerTemplateGenerator(simpleTemplateGenerator)
for test in tests:
# Load the PDB file.
pdb = PDBFile(os.path.join('systems', test['pdb_filename']))
# Parameterize system.
system = forcefield.createSystem(
pdb.topology, nonbondedMethod=test['nonbondedMethod'])
def test_Disulfides(self):
"""Test that various force fields handle disulfides correctly."""
pdb = PDBFile('systems/bpti.pdb')
for ff in ['amber99sb.xml', 'amber14-all.xml', 'charmm36.xml', 'amberfb15.xml', 'amoeba2013.xml']:
forcefield = ForceField(ff)
system = forcefield.createSystem(pdb.topology)
def test_residueTemplateGenerator(self):
"""Test the ability to add residue template generators to parameterize unmatched residues."""
def simpleTemplateGenerator(forcefield, residue):
"""\
Simple residue template generator.
This implementation uses the programmatic API to define residue templates.
NOTE: We presume we have already loaded the force definitions into ForceField.
"""
# Generate a unique prefix name for generating parameters.
from uuid import uuid4
template_name = uuid4()
# Create residue template.
template = ForceField._TemplateData(template_name)
for atom in residue.atoms():
typename = "XXX"
atom_template = ForceField._TemplateAtomData(atom.name, typename, atom.element)
template.atoms.append(atom_template)
for (atom1, atom2) in residue.internal_bonds():
template.addBondByName(atom1.name, atom2.name)
residue_atoms = [atom for atom in residue.atoms()]
for (atom1, atom2) in residue.external_bonds():
if atom1 in residue_atoms:
template.addExternalBondByName(atom1.name)
elif atom2 in residue_atoms:
template.addExternalBondByName(atom2.name)
# Register the template.
forcefield.registerResidueTemplate(template)
# Signal that we have successfully parameterized the residue.
return True
# Define forcefield parameters used by simpleTemplateGenerator.
# NOTE: This parameter definition file will currently only work for residues that either have
# no external bonds or external bonds to other residues parameterized by the simpleTemplateGenerator.
simple_ffxml_contents = """
<ForceField>
<AtomTypes>
<Type name="XXX" class="XXX" element="C" mass="12.0"/>
</AtomTypes>
<HarmonicBondForce>
<Bond type1="XXX" type2="XXX" length="0.1409" k="392459.2"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle type1="XXX" type2="XXX" type3="XXX" angle="2.09439510239" k="527.184"/>
</HarmonicAngleForce>
<NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
<Atom type="XXX" charge="0.000" sigma="0.315" epsilon="0.635"/>
</NonbondedForce>
</ForceField>"""
#
# Test where we generate parameters for only a ligand.
#
# Load the PDB file.
pdb = PDBFile(os.path.join("systems", "T4-lysozyme-L99A-p-xylene-implicit.pdb"))
# Create a ForceField object.
forcefield = ForceField("amber99sb.xml", "tip3p.xml", StringIO(simple_ffxml_contents))
# Add the residue template generator.
forcefield.registerTemplateGenerator(simpleTemplateGenerator)
# Parameterize system.
system = forcefield.createSystem(pdb.topology, nonbondedMethod=NoCutoff)
# TODO: Test energies are finite?
#
# Test for a few systems where we generate all parameters.
#
tests = [
{"pdb_filename": "alanine-dipeptide-implicit.pdb", "nonbondedMethod": NoCutoff},
{"pdb_filename": "lysozyme-implicit.pdb", "nonbondedMethod": NoCutoff},
{"pdb_filename": "alanine-dipeptide-explicit.pdb", "nonbondedMethod": CutoffPeriodic},
]
# Test all systems with separate ForceField objects.
for test in tests:
# Load the PDB file.
pdb = PDBFile(os.path.join("systems", test["pdb_filename"]))
# Create a ForceField object.
forcefield = ForceField(StringIO(simple_ffxml_contents))
# Add the residue template generator.
forcefield.registerTemplateGenerator(simpleTemplateGenerator)
# Parameterize system.
system = forcefield.createSystem(pdb.topology, nonbondedMethod=test["nonbondedMethod"])
# TODO: Test energies are finite?
# Now test all systems with a single ForceField object.
# Create a ForceField object.
forcefield = ForceField(StringIO(simple_ffxml_contents))
# Add the residue template generator.
forcefield.registerTemplateGenerator(simpleTemplateGenerator)
for test in tests:
# Load the PDB file.
pdb = PDBFile(os.path.join("systems", test["pdb_filename"]))
# Parameterize system.
system = forcefield.createSystem(pdb.topology, nonbondedMethod=test["nonbondedMethod"])
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
import simtk.openmm.app.element as elem
import simtk.openmm.app.forcefield as forcefield
from sys import stdout, argv
import mpidplugin
import numpy as np
pdb = PDBFile('mpidwater.pdb')
forcefield = ForceField('mpidwater.xml')
system = forcefield.createSystem(pdb.topology,
nonbondedMethod=LJPME,
nonbondedCutoff=8 * angstrom,
constraints=HBonds)
integrator = LangevinIntegrator(300 * kelvin, 1 / picosecond, 2 * femtoseconds)
#integrator = VerletIntegrator(1*femtoseconds)
# Make sure all the forces we expect are present
for force in range(system.getNumForces()):
print(system.getForce(force))
try:
myplatform = Platform.getPlatformByName('CUDA')
# Figure out which GPU to run on, i.e. did the user tell us?
deviceid = argv[1] if len(argv) > 1 else '0'
myproperties = {'DeviceIndex': deviceid, 'Precision': 'mixed'}
except:
print("CUDA NOT FOUND!!!!!!!!!!")
myplatform = None
deviceid = "N/A"