pdbatoms = list(pdb.topology.atoms())
labels = forcefield.labelMolecules([mol])[0]
for key, val in labels.items():
print(key)
for v in val:
anames = '-'.join([pdbatoms[i].name for i in v[0]])
anums = '-'.join([str(i) for i in v[0]])
print("%20s %20s %5s %-s" % (anames, anums, v[1], v[2]))
# The rest of this is not needed.
sys.exit()
# Create the OpenMM system
system = forcefield.createSystem(pdb.topology, [mol], nonbondedMethod=PME, nonbondedCutoff=1.0*unit.nanometers, rigidWater=True)
# Set up an OpenMM simulation
integrator = openmm.LangevinIntegrator(temperature, friction, time_step)
platform = openmm.Platform.getPlatformByName('CUDA')
simulation = Simulation(pdb.topology, system, integrator)
simulation.context.setPositions(pdb.positions)
simulation.context.setVelocitiesToTemperature(temperature)
netcdf_reporter = NetCDFReporter('water_traj.nc', trj_freq)
simulation.reporters.append(netcdf_reporter)
simulation.reporters.append(StateDataReporter('water_data.csv', data_freq, step=True, potentialEnergy=True, temperature= True, density=True))
print(simulation.context.getState(getEnergy=True).getPotentialEnergy())
simulation.minimizeEnergy()
print(simulation.context.getState(getEnergy=True).getPotentialEnergy())
def build_mixture_prmtop(gaff_mol2_filenames, box_filename, out_top, out_gro,
ffxml):
"""Analog of openmoltools.amber.build_mixture_prmtop which uses SMIRNOFF forcefield (from github.com/open-forcefield-group/smarty) to parameterize small molecules, rather than GAFF.
Parameters
----------
mol2_filenames : list(str)
Filenames of GAFF flavored mol2 files. Each must contain exactly
ONE solute.
box_filename : str
Filename of PDB containing an arbitrary box of the mol2 molecules.
out_top : str
output GROMACS topology filename. Should have suffix .top
out_gro : str
output gro filename. Should have suffix .gro
ffxml : str
filename containing input SMIRNOFF FFXML file for use in parameterizing the system
Returns
-------
success : bool
True or False as to success of operation
Notes
-----
This can be easily broken if there are missing, duplicated, or
inconsistent ligand residue names in your box, mol2, and frcmod files.
You can use mdtraj to edit the residue names with something like
this: trj.top.residue(0).name = "L1"
"""
from openeye import oechem
from openforcefield.typing.engines.smirnoff import ForceField, PME
from openforcefield.utils import read_molecules, get_data_filename, generateTopologyFromOEMol
# Read in molecules
oemols = []
for mol2file in set(gaff_mol2_filenames):
mol = oechem.OEGraphMol()
ifs = oechem.oemolistream(mol2file)
flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield
ifs.SetFlavor(oechem.OEFormat_MOL2, flavor)
oechem.OEReadMolecule(ifs, mol)
oechem.OETriposAtomNames(mol)
oemols.append(mol)
# Read in PDB file to get topology
pdb = app.PDBFile(box_filename)
# Load forcefield
ff = ForceField(ffxml)
# Construct system; charging not needed as mol2 files already have charges here
system = ff.createSystem(pdb.topology,
oemols,
nonbondedMethod=PME,
nonbondedCutoff=CUTOFF)
# Dump to AMBER format
structure = parmed.openmm.topsystem.load_topology(pdb.topology, system,
pdb.positions)
structure.save(out_top, overwrite=True)
structure.save(out_gro, overwrite=True)
return True
def convert_parameters(
source_directory="original/",
source_crd="full.crds",
source_top="full.topo",
destination_directory="generated/",
destination_crd="smirnoff.inpcrd",
destination_top="smirnoff.prmtop",
host_resname="MGO",
guest_resname="BAM",
atom_mapping=None,
residue_mapping=None,
):
create_pdb_with_conect(
solvated_pdb=source_directory + source_crd,
amber_prmtop=source_directory + source_top,
output_pdb=destination_directory + "full.pdb",
)
prune_conect(input_pdb="full.pdb",
output_pdb="full_conect.pdb",
path=destination_directory)
components = split_topology(file_name=destination_directory + "full.pdb")
hg_topology = create_host_guest_topology(components,
host_resname=host_resname,
guest_resname=guest_resname)
create_host_mol2(
solvated_pdb=destination_directory + "full.pdb",
amber_prmtop=source_directory + source_top,
mask=host_resname,
output_mol2=destination_directory + host_resname + ".mol2",
)
convert_mol2_to_sybyl_antechamber(
input_mol2=destination_directory + host_resname + ".mol2",
output_mol2=destination_directory + host_resname + "-sybyl.mol2",
ac_doctor=True,
)
host = load_mol2(
filename=destination_directory + host_resname + "-sybyl.mol2",
name=host_resname,
add_tripos=True,
)
guest = load_mol2(
filename=source_directory + guest_resname.lower() + ".mol2",
name=guest_resname,
add_tripos=False,
)
check_unique_atom_names(host)
check_unique_atom_names(guest)
molecules = [host, guest]
ff = ForceField("forcefield/smirnoff99Frosst.ffxml")
system = ff.createSystem(
hg_topology.topology,
molecules,
nonbondedCutoff=1.1 * unit.nanometer,
ewaldErrorTolerance=1e-4,
)
hg_structure = pmd.openmm.topsystem.load_topology(hg_topology.topology,
system,
hg_topology.positions)
check_bond_lengths(hg_structure, threshold=4)
try:
hg_structure.save(destination_directory + "hg.prmtop")
except OSError:
logging.warning(
"Check if the host-guest parameter file already exists...")
try:
hg_structure.save(destination_directory + "hg.inpcrd")
except OSError:
logging.warning(
"Check if the host-guest coordinate file already exists...")
extract_water_and_ions(
amber_prmtop=source_directory + source_top,
amber_inpcrd=source_directory + source_crd,
host_residue=":" + host_resname,
guest_residue=":" + guest_resname,
dummy=None,
output_pdb=destination_directory + "water_ions.pdb",
)
create_water_and_ions_parameters(
input_pdb="water_ions.pdb",
output_prmtop="water_ions.prmtop",
output_inpcrd="water_ions.inpcrd",
dummy_atoms=True,
path=destination_directory,
)
water_and_ions = pmd.amber.AmberParm(
destination_directory + "water_ions.prmtop",
xyz=destination_directory + "water_ions.inpcrd",
)
merged = mergeStructure(hg_structure, water_and_ions)
try:
merged.save(destination_directory + destination_top)
except:
logging.warning("Check if solvated parameter file already exists...")
try:
merged.save(destination_directory + destination_crd)
except:
logging.warning("Check if solvated coordinate file already exists...")
reference = pmd.load_file(source_directory + source_top,
source_directory + source_crd)
try:
reference.save(destination_directory + "reference.pdb")
reference.save(destination_directory + "reference.mol2")
except OSError:
logging.warning("Check if file exists...")
target = pmd.load_file(destination_directory + destination_top,
destination_directory + destination_crd)
try:
target.save(destination_directory + "target.pdb")
target.save(destination_directory + "target.mol2")
except OSError:
logging.warning("Check if file exists...")
if not atom_mapping:
reference_mol = load_mol2(destination_directory + "reference.mol2")
target_mol = load_mol2(destination_directory + "target.mol2")
atom_mapping = map_atoms(reference_mol, target_mol)
if not residue_mapping:
reference_mol = load_pdb(destination_directory + "reference.pdb")
target_mol = load_pdb(destination_directory + "target.pdb")
residue_mapping = map_residues(atom_mapping, reference_mol, target_mol)
# for file in ["mini.in", "therm1.in", "therm2.in", "eqnpt.in", "mdin"]:
# rewrite_amber_input_file(
# reference_input=source_directory + file,
# target_input=destination_directory + file,
# reference_to_target_mapping=residue_mapping,
# dt_override=False,
# target_prmtop=merged,
# )
# rewrite_restraints_file(
# reference_restraints=source_directory + "disang.rest",
# target_restraints=destination_directory + "disang.rest",
# reference_to_target_mapping=atom_mapping,
# )
# For some reason, this must come last, otherwise it gets removed again
merged.box = reference.box
try:
os.remove(destination_directory + destination_top)
os.remove(destination_directory + destination_crd)
except OSError:
pass
merged.save(destination_directory + destination_crd)
merged.save(destination_directory + destination_top)
return atom_mapping, residue_mapping
