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 test_modeller(self):
"""Test addition of hydrogens to a PDB file using modeller."""
pdb = app.PDBFile(
get_test_data("glu_ala_his_noH.pdb", "testsystems/tripeptides/"))
forcefield = app.ForceField("amber10-constph.xml", "ions_tip3p.xml",
"tip3p.xml")
modeller = app.Modeller(pdb.topology, pdb.positions)
modeller.addHydrogens(forcefield)
# Should have 59 hydrogens after adding them
assert modeller.topology.getNumAtoms() == 59
system = forcefield.createSystem(modeller.topology)
def xml_to_topology(topology_elem: etree.Element) -> app.Topology:
"""From a TopologyFile xml element, create a topology"""
text = topology_elem.text
fileio = StringIO(text)
topo_format = topology_elem.attrib["format"].lower()
if topo_format == "pdbx":
loaded = app.PDBxFile(fileio)
elif topo_format == "pdb":
loaded = app.PDBFile(fileio)
else:
raise ValueError(f"Unsupported topology format: '{topo_format}'.")
return loaded.getTopology()
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
def setup_peptide_implicit(name: str, minimize=True, createsim=True):
"""
Set up implicit solvent peptide
name - name of the peptide file. The folder "name_implicit" needs to exist,
and "name".pdb needs to exist in the folder.
minimize = Minimize the system before running (recommended)
Works only if simulation is created
createsim - instantiate simulation class
If False, minimization is not performed.
"""
peptide = SystemSetup()
peptide.temperature = 300.0 * unit.kelvin
# hahaha.pressure = 1.0 * unit.atmospheres
peptide.timestep = 2.0 * unit.femtoseconds
peptide.collision_rate = 1.0 / unit.picoseconds
peptide.pH = 7.0
peptide.perturbations_per_trial = 0 # instantaneous monte carlo
peptide.propagations_per_step = 1
testsystems = get_test_data("{}_implicit".format(name), "testsystems")
peptide.ffxml_files = os.path.join("amber10-constph.xml")
peptide.forcefield = ForceField(peptide.ffxml_files, "amber10-constph-obc2.xml")
peptide.pdbfile = app.PDBFile(os.path.join(testsystems, "{}.pdb".format(name)))
peptide.topology = peptide.pdbfile.topology
peptide.positions = peptide.pdbfile.getPositions(asNumpy=True)
# Quick fix for histidines in topology
# Openmm relabels them HIS, which leads to them not being detected as
# titratable. Renaming them fixes this.
for residue in peptide.topology.residues():
if residue.name == "HIS":
residue.name = "HIP"
peptide.constraint_tolerance = 1.0e-7
peptide.integrator = create_compound_gbaoab_integrator(peptide)
peptide.system = peptide.forcefield.createSystem(
peptide.topology, nonbondedMethod=app.NoCutoff, constraints=app.HBonds
)
peptide.drive = ForceFieldProtonDrive(
peptide.temperature,
peptide.topology,
peptide.system,
peptide.forcefield,
peptide.ffxml_files,
perturbations_per_trial=peptide.perturbations_per_trial,
propagations_per_step=peptide.propagations_per_step,
residues_by_name=None,
residues_by_index=None,
)
if createsim:
peptide.simulation = app.ConstantPHSimulation(
peptide.topology,
peptide.system,
peptide.integrator,
peptide.drive,
platform=TestSAMS.platform,
)
peptide.simulation.context.setPositions(peptide.positions)
peptide.context = peptide.simulation.context
if minimize:
peptide.simulation.minimizeEnergy()
return peptide
# coding=utf-8
"""
Adds hydrogens to 2HYY-noH.pdb
"""
from protons import app
from simtk.openmm import openmm
from simtk.unit import *
from protons.app.integrators import GBAOABIntegrator
# Load relevant template definitions for modeller, forcefield and topology
app.Modeller.loadHydrogenDefinitions('imatinib-hydrogens.xml')
forcefield = app.ForceField('amber10-constph.xml', 'gaff.xml', 'imatinib.xml', 'tip3p.xml', 'ions_tip3p.xml')
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)
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