From 983fdc4e4c948c17e40afe8e34af3ca920333aa8 Mon Sep 17 00:00:00 2001 From: George Hotz Date: Fri, 3 Apr 2020 11:16:21 -0700 Subject: [PATCH] fix solvent --- fold.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/fold.py b/fold.py index 24d1c33..50b2e22 100755 --- a/fold.py +++ b/fold.py @@ -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)