Comments (3)
from openmm.
Thanks, but when I am trying to reproduce this tutorial with my code:
from openmm import *
from openmm.app import *
from openmm.unit import *
from openff.toolkit.topology import Molecule, Topology
from openmmforcefields.generators import GAFFTemplateGenerator
modeller = pdbfile.PDBFile('topology.pdb')
forcefield = ForceField("amber14-all.xml","amber14/tip3pfb.xml")
ligand_file='6ny0_ligand.sdf'
gaff = GAFFTemplateGenerator(molecules=Molecule.from_file(ligand_file,allow_undefined_stereo=True))
forcefield.registerTemplateGenerator(gaff.generator)
system =
forcefield.createSystem(modeller.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=None)
solvent = set([a.index for a in modeller.topology.atoms() if a.residue.name in ('HOH', 'Cl','Na')])
#ligand = set([a.index for a in modeller.topology.atoms() if a.residue.name in ('UNK')])
protein = set([a.index for a in modeller.topology.atoms() if (a.index not in solvent)])
for force in system.getForces():
if isinstance(force, NonbondedForce):
force.setForceGroup(0)
force.addGlobalParameter("solute_coulomb_scale", 1)
force.addGlobalParameter("solute_lj_scale", 1)
force.addGlobalParameter("solvent_coulomb_scale", 1)
force.addGlobalParameter("solvent_lj_scale", 1)
for i in range(force.getNumParticles()):
charge, sigma, epsilon = force.getParticleParameters(i)
force.setParticleParameters(i, 0, 0, 0)
if i in protein:
force.addParticleParameterOffset("solute_coulomb_scale", i, charge, 0, 0)
force.addParticleParameterOffset("solute_lj_scale", i, 0, sigma, epsilon)
else:
force.addParticleParameterOffset("solvent_coulomb_scale", i, charge, 0, 0)
force.addParticleParameterOffset("solvent_lj_scale", i, 0, sigma, epsilon)
for i in range(force.getNumExceptions()):
p1, p2, chargeProd, sigma, epsilon = force.getExceptionParameters(i)
force.setExceptionParameters(i, p1, p2, 0, 0, 0)
else:
force.setForceGroup(2)
integrator = LangevinIntegrator(300*kelvin,5.0/picoseconds,2.0*femtoseconds)
context = Context(system, integrator)
context.setPositions(modeller.positions)
def energy(solute_coulomb_scale, solute_lj_scale, solvent_coulomb_scale, solvent_lj_scale):
context.setParameter("solute_coulomb_scale", solute_coulomb_scale)
context.setParameter("solute_lj_scale", solute_lj_scale)
context.setParameter("solvent_coulomb_scale", solvent_coulomb_scale)
context.setParameter("solvent_lj_scale", solvent_lj_scale)
return context.getState(getEnergy=True, groups={0}).getPotentialEnergy()
total_coulomb = energy(1, 0, 1, 0)
This Error occurs:
Traceback (most recent call last):
File "", line 1, in
File "/mnt/evafs/groups/sfglab/mwisniewski/anaconda3/envs/openmm/lib/python3.9/site-packages/openmm/openmm.py", line 12111, in getState
state = _openmm.Context_getState(self, types, enforcePeriodicBox, groups_mask)
openmm.OpenMMException: clSetKernelArg
Do you have an idea what I'm doing wrong?
from openmm.
That looks like an internal error of some sort. What OS, OpenMM version, and OpenCL implementation are you using?
Can you provide the input file so I can try running your script?
from openmm.
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from openmm.