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Commit 12fa5430 authored by peastman's avatar peastman
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Use correct parameters for nucleic acids with GBn2

parent 7f87c446
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wrappers/python/simtk/openmm/app/data/pdbNames.xml
View file @ 12fa5430
...@@ -239,19 +239,19 @@ ...@@ -239,19 +239,19 @@
<Atom name="HN2" alt1="2H" alt2="HT2" alt3="H2"/> <Atom name="HN2" alt1="2H" alt2="HT2" alt3="H2"/>
</Residue> </Residue>
<Residue name="UNK" type="Protein"/> <Residue name="UNK" type="Protein"/>
<Residue name="A" alt1="ADE" type="Nucleic"> <Residue name="A" alt1="ADE" alt2="A3" alt3="A5" type="Nucleic">
<Atom name="H61" alt1="1H6"/> <Atom name="H61" alt1="1H6"/>
<Atom name="H62" alt1="2H6"/> <Atom name="H62" alt1="2H6"/>
</Residue> </Residue>
<Residue name="G" alt1="GUA" type="Nucleic"> <Residue name="G" alt1="GUA" alt2="G3" alt3="G5" type="Nucleic">
<Atom name="H21" alt1="1H2"/> <Atom name="H21" alt1="1H2"/>
<Atom name="H22" alt1="2H2"/> <Atom name="H22" alt1="2H2"/>
</Residue> </Residue>
<Residue name="C" alt1="CYT" type="Nucleic"> <Residue name="C" alt1="CYT" alt2="C3" alt3="C5" type="Nucleic">
<Atom name="H41" alt1="1H4"/> <Atom name="H41" alt1="1H4"/>
<Atom name="H42" alt1="2H4"/> <Atom name="H42" alt1="2H4"/>
</Residue> </Residue>
<Residue name="U" alt1="URA" type="Nucleic"/> <Residue name="U" alt1="URA" alt2="U3" alt3="U5" type="Nucleic"/>
<Residue name="DA" alt1="DAD" alt2="DA3" alt3="DA5" type="Nucleic"> <Residue name="DA" alt1="DAD" alt2="DA3" alt3="DA5" type="Nucleic">
<Atom name="H61" alt1="1H6"/> <Atom name="H61" alt1="1H6"/>
<Atom name="H62" alt1="2H6"/> <Atom name="H62" alt1="2H6"/>
......
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ 12fa5430
...@@ -389,18 +389,20 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k ...@@ -389,18 +389,20 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions) "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions)
_SCREEN_PARAMETERS = { # normal, GBn, GBn2 _SCREEN_PARAMETERS = { # normal, GBn, GBn2, GBn2 nucleic
E.hydrogen : (0.85, 1.09085413633, 1.425952), E.hydrogen : (0.85, 1.09085413633, 1.425952, 1.696538),
E.carbon : (0.72, 0.48435382330, 1.058554), E.carbon : (0.72, 0.48435382330, 1.058554, 1.268902),
E.nitrogen : (0.79, 0.700147318409, 0.733599), E.nitrogen : (0.79, 0.700147318409, 0.733599, 1.4259728),
E.oxygen : (0.85, 1.06557401132, 1.061039), E.oxygen : (0.85, 1.06557401132, 1.061039, 0.1840098),
E.fluorine : (0.88, 0.5, 0.5), E.fluorine : (0.88, 0.5, 0.5, 0.5),
E.phosphorus : (0.86, 0.5, 0.5), E.phosphorus : (0.86, 0.5, 0.5, 1.5450597),
E.sulfur : (0.96, 0.602256336067, -0.703469), E.sulfur : (0.96, 0.602256336067, -0.703469, 0.05),
None : (0.8, 0.5, 0.5) # default None : (0.8, 0.5, 0.5, 0.5) # default
} }
_SCREEN_PARAMETERS[E.deuterium] = _SCREEN_PARAMETERS[E.hydrogen] _SCREEN_PARAMETERS[E.deuterium] = _SCREEN_PARAMETERS[E.hydrogen]
_NUCLEIC_ACID_RESIDUES = ['A', 'C', 'G', 'U', 'DA', 'DC', 'DG', 'DT']
def _screen_parameter(atom): def _screen_parameter(atom):
return _SCREEN_PARAMETERS.get(atom.element, _SCREEN_PARAMETERS[None]) return _SCREEN_PARAMETERS.get(atom.element, _SCREEN_PARAMETERS[None])
...@@ -873,7 +875,16 @@ class GBSAGBn2Force(GBSAGBnForce): ...@@ -873,7 +875,16 @@ class GBSAGBn2Force(GBSAGBnForce):
E.oxygen: [0.867814, 0.876635, 0.387882], E.oxygen: [0.867814, 0.876635, 0.387882],
E.sulfur: [0.867814, 0.876635, 0.387882], E.sulfur: [0.867814, 0.876635, 0.387882],
} }
_default_atom_params = [0.8, 4.85, 0.5] _atom_params_nucleic = {
E.hydrogen: [0.537050, 0.362861, 0.116704],
E.deuterium: [0.537050, 0.362861, 0.116704],
E.carbon: [0.331670, 0.196842, 0.093422],
E.nitrogen: [0.686311, 0.463189, 0.138722],
E.oxygen: [0.606344, 0.463006, 0.142262],
E.sulfur: [0.606344, 0.463006, 0.142262],
E.phosphorus: [0.418365, 0.290054, 0.1064245],
}
_default_atom_params = [1.0, 0.8, 4.851]
@classmethod @classmethod
def getStandardParameters(cls, topology): def getStandardParameters(cls, topology):
...@@ -897,11 +908,20 @@ class GBSAGBn2Force(GBSAGBnForce): ...@@ -897,11 +908,20 @@ class GBSAGBn2Force(GBSAGBnForce):
radii = numpy.empty([natoms,5], numpy.double) radii = numpy.empty([natoms,5], numpy.double)
radii[:,0] = _mbondi3_radii(topology)/10 radii[:,0] = _mbondi3_radii(topology)/10
for atom, rad in zip(topology.atoms(), radii): for atom, rad in zip(topology.atoms(), radii):
if atom.residue.name in _NUCLEIC_ACID_RESIDUES:
rad[1] = _screen_parameter(atom)[3]
rad[2:] = cls._atom_params_nucleic.get(atom.element, cls._default_atom_params)
else:
rad[1] = _screen_parameter(atom)[2] rad[1] = _screen_parameter(atom)[2]
rad[2:] = cls._atom_params.get(atom.element, cls._default_atom_params) rad[2:] = cls._atom_params.get(atom.element, cls._default_atom_params)
else: else:
radii = [[r/10, 0, 0, 0, 0] for r in _mbondi3_radii(topology)] radii = [[r/10, 0, 0, 0, 0] for r in _mbondi3_radii(topology)]
for atom, rad in zip(topology.atoms(), radii): for atom, rad in zip(topology.atoms(), radii):
if atom.residue.name in _NUCLEIC_ACID_RESIDUES:
rad[1] = _screen_parameter(atom)[3]
for i, p in enumerate(cls._atom_params_nucleic.get(atom.element, cls._default_atom_params)):
rad[2+i] = p
else:
rad[1] = _screen_parameter(atom)[2] rad[1] = _screen_parameter(atom)[2]
for i, p in enumerate(cls._atom_params.get(atom.element, cls._default_atom_params)): for i, p in enumerate(cls._atom_params.get(atom.element, cls._default_atom_params)):
rad[2+i] = p rad[2+i] = p
......
wrappers/python/tests/TestAmberPrmtopFile.py
View file @ 12fa5430
...@@ -384,5 +384,21 @@ class TestAmberPrmtopFile(unittest.TestCase): ...@@ -384,5 +384,21 @@ class TestAmberPrmtopFile(unittest.TestCase):
self.assertRaises(ValueError, lambda: f.addParticle([0, 0.9, 0.5])) self.assertRaises(ValueError, lambda: f.addParticle([0, 0.9, 0.5]))
self.assertRaises(ValueError, lambda: f.addParticle([0, 0.21, 0.5])) self.assertRaises(ValueError, lambda: f.addParticle([0, 0.21, 0.5]))
def testNucleicGBParametes(self):
"""Test that correct GB parameters are used for nucleic acids."""
prmtop = AmberPrmtopFile('systems/DNA_mbondi3.prmtop')
inpcrd = AmberInpcrdFile('systems/DNA_mbondi3.inpcrd')
sanderEnergy = [-19223.87993545, -19527.40433175, -19788.1070698]
for solvent, expectedEnergy in zip([OBC2, GBn, GBn2], sanderEnergy):
system = prmtop.createSystem(implicitSolvent=solvent, gbsaModel=None)
for f in system.getForces():
if isinstance(f, CustomGBForce) or isinstance(f, GBSAOBCForce):
f.setForceGroup(1)
integrator = VerletIntegrator(0.001)
context = Context(system, integrator, Platform.getPlatformByName('Reference'))
context.setPositions(inpcrd.positions)
energy = context.getState(getEnergy=True, groups={1}).getPotentialEnergy().value_in_unit(kilojoules_per_mole)
self.assertAlmostEqual(energy, expectedEnergy, delta=5e-4*abs(energy))
if __name__ == '__main__': if __name__ == '__main__':
unittest.main() unittest.main()
wrappers/python/tests/systems/DNA_mbondi3.inpcrd 0 → 100644
View file @ 12fa5430
default_name
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wrappers/python/tests/systems/DNA_mbondi3.prmtop 0 → 100644
View file @ 12fa5430
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