def setup_viologen_implicit():
"""
Set up viologen in implicit solvent
"""
viologen = SystemSetup()
viologen.temperature = 300.0 * unit.kelvin
viologen.pressure = 1.0 * unit.atmospheres
viologen.timestep = 1.0 * unit.femtoseconds
viologen.collision_rate = 1.0 / unit.picoseconds
viologen.pH = 7.0
testsystems = get_test_data("viologen", "testsystems")
viologen.ffxml_files = os.path.join(testsystems,
"viologen-protons.ffxml")
viologen.gaff = os.path.join(testsystems, "gaff.xml")
viologen.forcefield = ForceField(viologen.gaff, "gaff-obc2.xml",
viologen.ffxml_files)
viologen.pdbfile = app.PDBFile(
os.path.join(testsystems, "viologen-vacuum.pdb"))
viologen.topology = viologen.pdbfile.topology
viologen.positions = viologen.pdbfile.getPositions(asNumpy=True)
viologen.constraint_tolerance = 1.0e-7
viologen.integrator = openmm.LangevinIntegrator(
viologen.temperature, viologen.collision_rate, viologen.timestep)
viologen.integrator.setConstraintTolerance(
viologen.constraint_tolerance)
viologen.system = viologen.forcefield.createSystem(
viologen.topology,
nonbondedMethod=app.NoCutoff,
constraints=app.HBonds)
viologen.cooh1 = { # indices in topology of the first cooh group
"HO": 56,
"OH": 0,
"CO": 1,
"OC": 2,
"R": 3,
}
viologen.cooh2 = { # indices in topology of the second cooh group
"HO": 57,
"OH": 27,
"CO": 25,
"OC": 26,
"R": 24,
}
viologen.simulation = app.Simulation(
viologen.topology,
viologen.system,
viologen.integrator,
TestCarboxylicAcid.platform,
)
viologen.simulation.context.setPositions(viologen.positions)
viologen.context = viologen.simulation.context
viologen.perturbations_per_trial = 10
viologen.propagations_per_step = 1
return viologen
def setup_amino_acid_water(three_letter_code):
"""
Set up glutamic acid in water
"""
if three_letter_code not in ["glh", "ash"]:
raise ValueError("Amino acid not available.")
aa = SystemSetup()
aa.temperature = 300.0 * unit.kelvin
aa.pressure = 1.0 * unit.atmospheres
aa.timestep = 1.0 * unit.femtoseconds
aa.collision_rate = 1.0 / unit.picoseconds
aa.pH = 7.0
testsystems = get_test_data("amino_acid", "testsystems")
aa.ffxml_files = "amber10-constph.xml"
aa.forcefield = ForceField(aa.ffxml_files, "tip3p.xml")
aa.pdbfile = app.PDBFile(
os.path.join(testsystems, "{}.pdb".format(three_letter_code)))
aa.topology = aa.pdbfile.topology
aa.positions = aa.pdbfile.getPositions(asNumpy=True)
aa.constraint_tolerance = 1.0e-7
aa.integrator = create_compound_gbaoab_integrator(aa)
aa.integrator.setConstraintTolerance(aa.constraint_tolerance)
aa.system = aa.forcefield.createSystem(
aa.topology,
nonbondedMethod=app.PME,
nonbondedCutoff=1.0 * unit.nanometers,
constraints=app.HBonds,
rigidWater=True,
ewaldErrorTolerance=0.0005,
)
aa.system.addForce(
openmm.MonteCarloBarostat(aa.pressure, aa.temperature, 25))
aa.simulation = app.Simulation(aa.topology, aa.system, aa.integrator,
TestCarboxylicAcid.platform)
aa.simulation.context.setPositions(aa.positions)
aa.context = aa.simulation.context
aa.perturbations_per_trial = 1000
aa.propagations_per_step = 1
return aa
pdb = app.PDBFile('2HYY-noH.pdb')
modeller = app.Modeller(pdb.topology, pdb.positions)
# The pdb contains solvent but not the right ions.
# This would mean we need to equilibrate again even if we just add new ions.
# In this case its easiest to just delete and re-add the solvent with the right amount of ions
modeller.deleteWater()
ions = [ atom for atom in modeller.topology.atoms() if atom.element.symbol in ['Cl', 'Na'] ]
modeller.delete(ions)
modeller.addHydrogens(forcefield=forcefield)
modeller.addSolvent(forcefield, model='tip3p', padding=1.0*nanometers, positiveIon='Na+', negativeIon='Cl-', ionicStrength=120*millimolar, neutralize=True)
system = forcefield.createSystem(modeller.topology, nonbondedMethod=app.PME, nonbondedCutoff=1.0 * nanometers,
constraints=app.HBonds, rigidWater=True,
ewaldErrorTolerance=0.0005)
system.addForce(openmm.MonteCarloBarostat(1.0 * atmosphere, 300.0 * kelvin))
simulation = app.Simulation(modeller.topology, system, GBAOABIntegrator() )
simulation.context.setPositions(modeller.positions)
rename_res = {"HIS": "HIP", "ASP":"AS4", "GLU":"GL4"}
for resi in modeller.topology.residues():
if resi.name in rename_res:
resi.name = rename_res[resi.name]
app.PDBFile.writeFile(modeller.topology, simulation.context.getState(getPositions=True).getPositions(),
open('2HYY-H.pdb', 'w'))
def setup_viologen_water():
"""
Set up viologen in water
"""
viologen = SystemSetup()
viologen.temperature = 300.0 * unit.kelvin
viologen.pressure = 1.0 * unit.atmospheres
viologen.timestep = 1.0 * unit.femtoseconds
viologen.collision_rate = 1.0 / unit.picoseconds
viologen.pH = 7.0
testsystems = get_test_data("viologen", "testsystems")
viologen.ffxml_files = os.path.join(testsystems,
"viologen-protons-cooh.ffxml")
viologen.gaff = os.path.join(testsystems, "gaff.xml")
viologen.forcefield = ForceField(viologen.gaff, viologen.ffxml_files,
"tip3p.xml")
viologen.pdbfile = app.PDBFile(
os.path.join(testsystems, "viologen-solvated.pdb"))
viologen.topology = viologen.pdbfile.topology
viologen.positions = viologen.pdbfile.getPositions(asNumpy=True)
viologen.constraint_tolerance = 1.0e-7
viologen.integrator = create_compound_gbaoab_integrator(viologen)
viologen.integrator.setConstraintTolerance(
viologen.constraint_tolerance)
viologen.system = viologen.forcefield.createSystem(
viologen.topology,
nonbondedMethod=app.PME,
nonbondedCutoff=1.0 * unit.nanometers,
constraints=app.HBonds,
rigidWater=True,
ewaldErrorTolerance=0.0005,
)
viologen.system.addForce(
openmm.MonteCarloBarostat(viologen.pressure, viologen.temperature,
25))
viologen.cooh1 = { # indices in topology of the first cooh group
"HO": 56,
"OH": 1,
"CO": 0,
"OC": 2,
"R": 3,
}
viologen.cooh2 = { # indices in topology of the second cooh group
"HO": 57,
"OH": 27,
"CO": 25,
"OC": 26,
"R": 24,
}
viologen.simulation = app.Simulation(
viologen.topology,
viologen.system,
viologen.integrator,
TestCarboxylicAcid.platform,
)
viologen.simulation.context.setPositions(viologen.positions)
viologen.context = viologen.simulation.context
viologen.perturbations_per_trial = 1000
viologen.propagations_per_step = 1
return viologen