def create_ffxml_simulation(molecule_name, gaff_mol2_filename,
frcmod_filename):
"""Process a gaff mol2 file and frcmod file using the XML conversion, returning an OpenMM simulation.
Parameters
----------
molecule_name : str
The name of the molecule
gaff_mol2_filename : str
The name of the gaff mol2 file
frcmod_filename : str
The name of the gaff frcmod file
Returns
-------
simulation : openmm.app.Simulation
A functional simulation object for simulating your molecule
"""
# Generate ffxml file.
amber = import_("openmoltools.amber")
GAFF_DAT_FILENAME = amber.find_gaff_dat()
parser = amber_parser.AmberParser()
parser.parse_filenames(
[GAFF_DAT_FILENAME, gaff_mol2_filename, frcmod_filename])
ffxml_filename = molecule_name + '.ffxml'
create_ffxml_file([gaff_mol2_filename], [frcmod_filename], ffxml_filename)
traj = md.load(gaff_mol2_filename) # Read mol2 file.
positions = traj.openmm_positions(
0
) # Extract OpenMM-united positions of first (and only) trajectory frame
topology = traj.top.to_openmm()
# Create System object.
forcefield = app.ForceField(ffxml_filename)
system = forcefield.createSystem(topology,
nonbondedMethod=app.NoCutoff,
constraints=None,
implicitSolvent=None)
# Create integrator.
timestep = 1.0 * units.femtoseconds
integrator = simtk.openmm.VerletIntegrator(timestep)
# Create simulation.
platform = simtk.openmm.Platform.getPlatformByName("Reference")
simulation = app.Simulation(topology,
system,
integrator,
platform=platform)
simulation.context.setPositions(positions)
return simulation
def create_ffxml_file(gaff_mol2_filenames,
frcmod_filenames,
ffxml_filename=None,
override_mol2_residue_name=None):
"""Process multiple gaff mol2 files and frcmod files using the XML conversion and write to an XML file.
Parameters
----------
gaff_mol2_filenames : list of str
The names of the gaff mol2 files
frcmod_filenames : str
The names of the gaff frcmod files
ffxml_filename : str, optional, default=None
Optional name of output ffxml file to generate. If None, no file
will be generated.
override_mol2_residue_name : str, default=None
If given, use this name to override mol2 residue names.
Returns
-------
ffxml_stringio : str
StringIO representation of ffxml file containing residue entries for each molecule.
"""
# Generate ffxml file.
parser = amber_parser.AmberParser(
override_mol2_residue_name=override_mol2_residue_name)
amber = import_("openmoltools.amber")
GAFF_DAT_FILENAME = amber.find_gaff_dat()
filenames = [GAFF_DAT_FILENAME]
filenames.extend([filename for filename in gaff_mol2_filenames])
filenames.extend([filename for filename in frcmod_filenames])
parser.parse_filenames(filenames)
ffxml_stream = parser.generate_xml()
if ffxml_filename is not None:
outfile = open(ffxml_filename, 'w')
outfile.write(ffxml_stream.read())
outfile.close()
ffxml_stream.seek(0)
return ffxml_stream
import sys
from openmoltools import amber_parser
if __name__ == "__main__":
if len(sys.argv[1:]) <= 1:
print(
"""Usage: processAmberForceField.py some_path/gaff.dat ligand_name.mol2 ligand_name.frcmod
""")
else:
parser = amber_parser.AmberParser()
parser.parse_filenames(sys.argv[1:])
stream = parser.generate_xml()
print(stream.read())