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fix solvent
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@geohot
geohot committed Apr 3, 2020
1 parent a71d6da commit 983fdc4
Showing 1 changed file with 5 additions and 2 deletions.
7 changes: 5 additions & 2 deletions fold.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,13 +38,16 @@
pdb = PDBFile(args.pdb)

#forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
forcefield = ForceField('amber03.xml', 'tip3p.xml')
forcefield = ForceField('amber03.xml', 'amber03_obc.xml')

modeller = Modeller(pdb.topology, pdb.positions)
modeller.addHydrogens(forcefield)
print(modeller.topology)

system = forcefield.createSystem(modeller.topology, nonbondedMethod=NoCutoff, nonbondedCutoff=1*nanometer, constraints=HBonds)
system = forcefield.createSystem(modeller.topology,
implicitSolvent=OBC2, # matches https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2980750/#bib39
nonbondedMethod=NoCutoff, nonbondedCutoff=1*nanometer,
constraints=HBonds)
integrator = LangevinIntegrator(args.temp*kelvin, 1/picosecond, 2*femtoseconds)
simulation = Simulation(modeller.topology, system, integrator, platform)
simulation.context.setPositions(modeller.positions)
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