def omm_system(input_sdf,
input_system,
forcefield,
input_path,
ff_files=[],
template_ff='gaff-2.11'):
from openmmforcefields.generators import SystemGenerator, GAFFTemplateGenerator
from openff.toolkit.topology import Molecule
# maybe possible to add same parameters that u give forcefield.createSystem() function
forcefield_kwargs ={'constraints' : app.HBonds,
'rigidWater' : True,
'removeCMMotion' : False,
'hydrogenMass' : 4*amu }
system_generator = SystemGenerator(forcefields=ff_files,
small_molecule_forcefield=template_ff,
forcefield_kwargs=forcefield_kwargs,
cache='db.json')
input_sdfs=[]
for idx, sdf in enumerate(input_sdf, 1):
path_sdf=f'{input_path}/{sdf}'
if not os.path.exists(path_sdf):
print(f'\tFile {path_sdf} not found!')
else:
print(f'\tAdding extra SDF file {idx} to pre-system: {path_sdf}')
input_sdfs.append(path_sdf)
molecules = Molecule.from_file(*input_sdfs, file_format='sdf')
print(molecules)
system = system_generator.create_system(topology=input_system.topology)#, molecules=molecules)
gaff = GAFFTemplateGenerator(molecules=molecules, forcefield=template_ff)
gaff.add_molecules(molecules)
print(gaff)
forcefield.registerTemplateGenerator(gaff.generator)
#forcefield.registerResidueTemplate(template)
print(system)
print(forcefield)
return system, forcefield
""" Assemble the holo-complex """
molAPO = PDBFile(f'{PDB_DIR}/{SEED_PDB}.fab.fixed.pdb')
molLIG = PDBFile(f'{PDB_DIR}/{TARGET_CID}.pdb')
molSMI = Chem.MolToSmiles(
molPROBE, isomericSmiles=True, allBondsExplicit=True)
model = Modeller(molAPO.topology, molAPO.getPositions())
model.add(molLIG.topology, molLIG.getPositions())
with open('holo.pdb', 'w+') as outfile:
PDBFile.writeFile(model.topology, model.getPositions(), outfile)
""" Parameterize the holo-complex """
GAFFForceField = GAFFTemplateGenerator.INSTALLED_FORCEFIELDS[-1]
GAFFTemplate = GAFFTemplateGenerator(forcefield=GAFFForceField)
GAFFTemplate.add_molecules(
Molecule.from_smiles(molSMI, allow_undefined_stereo=True))
forcefield = app.ForceField('amber14/protein.ff14SB.xml')
forcefield.registerTemplateGenerator(GAFFTemplate.generator)
system00 = forcefield.createSystem(model.topology)
""" Minimize the holo-complex """
holo = app.PDBFile('holo.pdb')
integrator = LangevinIntegrator(
LANGE_TEMPERATURE, LANGE_FRICTION, LANGE_STEPSIZE)
integrator.setConstraintTolerance(LANGE_TOLERANCE)
simulation = Simulation(holo.topology, system00, integrator)
simulation.context.setPositions(holo.getPositions())
simulation.minimizeEnergy(ENERGY_TOLERANCE, MAX_ENERGY_ITERS)