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Commit 5bed3590 authored by Peter Eastman's avatar Peter Eastman
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Fixed CHARMM parser to work with changes to custom GB models

parent 71b67421
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Showing with 237 additions and 13 deletions
wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ 5bed3590
...@@ -43,7 +43,7 @@ import simtk.unit as u ...@@ -43,7 +43,7 @@ import simtk.unit as u
from simtk.openmm.app import (forcefield as ff, Topology, element) from simtk.openmm.app import (forcefield as ff, Topology, element)
from simtk.openmm.app.amberprmtopfile import HCT, OBC1, OBC2, GBn, GBn2 from simtk.openmm.app.amberprmtopfile import HCT, OBC1, OBC2, GBn, GBn2
from simtk.openmm.app.internal.customgbforces import (GBSAHCTForce, from simtk.openmm.app.internal.customgbforces import (GBSAHCTForce,
GBSAOBC1Force, GBSAOBC2Force, GBSAGBnForce, GBSAGBn2Force) GBSAOBC1Force, GBSAOBC2Force, GBSAGBnForce, GBSAGBn2Force, convertParameters)
# CHARMM imports # CHARMM imports
from simtk.openmm.app.internal.charmm.topologyobjects import ( from simtk.openmm.app.internal.charmm.topologyobjects import (
ResidueList, AtomList, TrackedList, Bond, Angle, Dihedral, ResidueList, AtomList, TrackedList, Bond, Angle, Dihedral,
...@@ -1374,6 +1374,7 @@ class CharmmPsfFile(object): ...@@ -1374,6 +1374,7 @@ class CharmmPsfFile(object):
if implicitSolvent is not None: if implicitSolvent is not None:
if verbose: print('Adding GB parameters...') if verbose: print('Adding GB parameters...')
gb_parms = self._get_gb_params(implicitSolvent) gb_parms = self._get_gb_params(implicitSolvent)
gb_parms = convertParameters(gb_parms, str(implicitSolvent))
# If implicitSolventKappa is None, compute it from salt # If implicitSolventKappa is None, compute it from salt
# concentration # concentration
......
wrappers/python/tests/TestCharmmFiles.py
View file @ 5bed3590
...@@ -69,21 +69,9 @@ class TestCharmmFiles(unittest.TestCase): ...@@ -69,21 +69,9 @@ class TestCharmmFiles(unittest.TestCase):
system = self.psf_x.createSystem(self.params, implicitSolvent=GBn, system = self.psf_x.createSystem(self.params, implicitSolvent=GBn,
solventDielectric=50.0, solventDielectric=50.0,
soluteDielectric = 0.9) soluteDielectric = 0.9)
found_matching_solvent_dielectric=False
found_matching_solute_dielectric=False
for force in system.getForces(): for force in system.getForces():
if isinstance(force, CustomGBForce):
for i in range(force.getNumGlobalParameters()):
if force.getGlobalParameterName(i) == 'solventDielectric':
if force.getGlobalParameterDefaultValue(i) == 50.0:
found_matching_solvent_dielectric = True
elif force.getGlobalParameterName(i) == 'soluteDielectric':
if force.getGlobalParameterDefaultValue(i) == 0.9:
found_matching_solute_dielectric = True
if isinstance(force, NonbondedForce): if isinstance(force, NonbondedForce):
self.assertEqual(force.getReactionFieldDielectric(), 1.0) self.assertEqual(force.getReactionFieldDielectric(), 1.0)
self.assertTrue(found_matching_solvent_dielectric and
found_matching_solute_dielectric)
def test_HydrogenMass(self): def test_HydrogenMass(self):
"""Test that altering the mass of hydrogens works correctly.""" """Test that altering the mass of hydrogens works correctly."""
...@@ -127,6 +115,26 @@ class TestCharmmFiles(unittest.TestCase): ...@@ -127,6 +115,26 @@ class TestCharmmFiles(unittest.TestCase):
ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole) ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene, 15490.0033559, delta=0.05) self.assertAlmostEqual(ene, 15490.0033559, delta=0.05)
def test_ImplicitSolventForces(self):
"""Compute forces for different implicit solvent types, and compare them to ones generated with a previous version of OpenMM to ensure they haven't changed."""
solventType = [HCT, OBC1, OBC2, GBn, GBn2]
nonbondedMethod = [NoCutoff, CutoffNonPeriodic, CutoffNonPeriodic, NoCutoff, NoCutoff]
salt = [0.0, 0.0, 0.5, 0.5, 0.0]*(moles/liter)
file = ['HCT_NoCutoff', 'OBC1_NonPeriodic', 'OBC2_NonPeriodic_Salt', 'GBn_NoCutoff_Salt', 'GBn2_NoCutoff']
for i in range(5):
system = self.psf_c.createSystem(self.params, implicitSolvent=solventType[i], nonbondedMethod=nonbondedMethod[i], implicitSolventSaltConc=salt[i])
integrator = VerletIntegrator(0.001)
context = Context(system, integrator, Platform.getPlatformByName("CPU"))
context.setPositions(self.pdb.positions)
state1 = context.getState(getForces=True)
#out = open('systems/ala-ala-ala-implicit-forces/'+file[i]+'.xml', 'w')
#out.write(XmlSerializer.serialize(state1))
#out.close()
state2 = XmlSerializer.deserialize(open('systems/ala-ala-ala-implicit-forces/'+file[i]+'.xml').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-4)
if __name__ == '__main__': if __name__ == '__main__':
unittest.main() unittest.main()
wrappers/python/tests/systems/ala-ala-ala-implicit-forces/GBn2_NoCutoff.xml 0 → 100644
View file @ 5bed3590
<?xml version="1.0" ?>
<State time="0" type="State" version="1">
<PeriodicBoxVectors>
<A x="2" y="0" z="0"/>
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</Forces>
</State>
wrappers/python/tests/systems/ala-ala-ala-implicit-forces/GBn_NoCutoff_Salt.xml 0 → 100644
View file @ 5bed3590
<?xml version="1.0" ?>
<State time="0" type="State" version="1">
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wrappers/python/tests/systems/ala-ala-ala-implicit-forces/HCT_NoCutoff.xml 0 → 100644
View file @ 5bed3590
<?xml version="1.0" ?>
<State time="0" type="State" version="1">
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wrappers/python/tests/systems/ala-ala-ala-implicit-forces/OBC1_NonPeriodic.xml 0 → 100644
View file @ 5bed3590
<?xml version="1.0" ?>
<State time="0" type="State" version="1">
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wrappers/python/tests/systems/ala-ala-ala-implicit-forces/OBC2_NonPeriodic_Salt.xml 0 → 100644
View file @ 5bed3590
<?xml version="1.0" ?>
<State time="0" type="State" version="1">
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