# receptor_atoms = range(0,12) # benzene
# ligand_atoms = range(12,27) # toluene
receptor_atoms = range(0,2603) # T4 lysozyme L99A
ligand_atoms = range(2603,2621) # p-xylene
platform_names = ['Reference', 'Cuda', 'OpenCL']
platform_names = ['Cuda', 'OpenCL']
# Create force type variants of systems.
force_types = ['standard', 'softcore-full', 'softcore-annihilated', 'custom-full', 'custom-annihilated'] # Different force types
system_types = ['complex', 'receptor']
systems = dict()
for system_type in system_types:
systems[system_type] = dict()
# Load standard systems.
import simtk.pyopenmm.amber.amber_file_parser as amber
systems['complex']['standard'] = amber.readAmberSystem(complex_prmtop_filename, mm=openmm, gbmodel=gbmodel, shake='h-bonds')
systems['receptor']['standard'] = amber.readAmberSystem(receptor_prmtop_filename, mm=openmm, gbmodel=gbmodel, shake='h-bonds')
# Create softcore force type variants.
for system_type in system_types:
systems[system_type]['softcore-full'] = build_softcore_system(systems[system_type]['standard'], receptor_atoms, ligand_atoms, 1.0, 1.0, 1.0)
systems[system_type]['softcore-annihilated'] = build_softcore_system(systems[system_type]['standard'], receptor_atoms, ligand_atoms, 0.0, 0.0, 0.0)
# Create custom force type variants.
for system_type in system_types:
systems[system_type]['custom-full'] = build_custom_system(systems[system_type]['standard'], receptor_atoms, ligand_atoms, 1.0, 1.0, 1.0)
systems[system_type]['custom-annihilated'] = build_custom_system(systems[system_type]['standard'], receptor_atoms, ligand_atoms, 0.0, 0.0, 0.0)
# Read coordinates.
coordinates = dict()
coordinates['complex'] = amber.readAmberCoordinates(complex_crd_filename)
coordinates['receptor'] = coordinates['complex'][receptor_atoms,:]
# Create force type variants of systems.
force_types = [
'standard', 'softcore lambda=1', 'softcore lambda=0',
'custom lambda=1', 'custom lambda=0'
] # Different force types
system_types = ['complex', 'receptor', 'ligand']
systems = dict()
for system_type in system_types:
systems[system_type] = dict()
# Load standard systems.
import simtk.pyopenmm.amber.amber_file_parser as amber
systems['complex']['standard'] = amber.readAmberSystem(
complex_prmtop_filename,
mm=openmm,
gbmodel=gbmodel,
nonbondedCutoff=None,
nonbondedMethod='no-cutoff',
shake='h-bonds')
systems['receptor']['standard'] = amber.readAmberSystem(
receptor_prmtop_filename,
mm=openmm,
gbmodel=gbmodel,
nonbondedCutoff=None,
nonbondedMethod='no-cutoff',
shake='h-bonds')
systems['ligand']['standard'] = amber.readAmberSystem(
ligand_prmtop_filename,
mm=openmm,
gbmodel=gbmodel,
nonbondedCutoff=None,
# receptor_crd_filename = 'receptor-minimized.crd'
ligand_prmtop_filename = 'ligand.prmtop'
ligand_crd_filename = 'ligand.crd'
# ligand_crd_filename = 'ligand-minimized.crd'
platform_names = ['Reference', 'Cuda', 'OpenCL']
platform_names = ['Cuda', 'OpenCL']
# Create force type variants of systems.
force_types = ['standard', 'softcore lambda=1', 'softcore lambda=0', 'custom lambda=1', 'custom lambda=0'] # Different force types
system_types = ['complex', 'receptor', 'ligand']
systems = dict()
for system_type in system_types:
systems[system_type] = dict()
# Load standard systems.
import simtk.pyopenmm.amber.amber_file_parser as amber
systems['complex']['standard'] = amber.readAmberSystem(complex_prmtop_filename, mm=openmm, gbmodel=gbmodel, nonbondedCutoff=None, nonbondedMethod='no-cutoff', shake='h-bonds')
systems['receptor']['standard'] = amber.readAmberSystem(receptor_prmtop_filename, mm=openmm, gbmodel=gbmodel, nonbondedCutoff=None, nonbondedMethod='no-cutoff', shake='h-bonds')
systems['ligand']['standard'] = amber.readAmberSystem(ligand_prmtop_filename, mm=openmm, gbmodel=gbmodel, nonbondedCutoff=None, nonbondedMethod='no-cutoff', shake='h-bonds')
# Determine number of particles.
nparticles = dict()
for system_type in system_types:
nparticles[system_type] = systems[system_type]['standard'].getNumParticles()
nparticles['ligand'] = nparticles['complex'] - nparticles['receptor']
receptor_atoms = range(0,nparticles['receptor'])
ligand_atoms = range(nparticles['receptor'], nparticles['complex'])
# Add harmonic protein-ligand restraint.
add_restraint = True
iatom = receptor_atoms[0]
if __name__ == "__main__":
# Create system
system = openmm.System()
timestep = 1.0 * units.femtoseconds
# Set whether to use GB model or not.
gbmodel = 'OBC' # use OBC GBSA (gives finite error)
#gbmodel = 'none' # no solvent model (gives zero error)
# Load amber system for complex.
prmtop_filename = 'complex.prmtop'
crd_filename = 'complex.crd'
import simtk.pyopenmm.amber.amber_file_parser as amber
complex_system = amber.readAmberSystem(prmtop_filename,
mm=openmm,
gbmodel=gbmodel,
shake='h-bonds')
complex_coordinates = amber.readAmberCoordinates(crd_filename)
# Load amber system for receptor only.
prmtop_filename = 'receptor.prmtop'
crd_filename = 'receptor.crd'
receptor_system = amber.readAmberSystem(prmtop_filename,
mm=openmm,
gbmodel=gbmodel,
shake='h-bonds')
receptor_coordinates = amber.readAmberCoordinates(crd_filename)
# Create alchemically-modified system where ligand is turned off.
receptor_atoms = range(0, 2603)
ligand_atoms = range(2603, 2621)
temperature = 300 * units.kelvin
kB = units.BOLTZMANN_CONSTANT_kB * units.AVOGADRO_CONSTANT_NA
kT = kB * temperature
beta = 1.0 / kT
gbmodel = 'OBC'
#gbmodel = None
# Load amber system.
receptor_prmtop_filename = 'receptor.prmtop'
complex_prmtop_filename = 'complex.prmtop'
ligand_prmtop_filename = 'ligand.prmtop'
complex_crd_filename = 'complex.crd'
import simtk.pyopenmm.amber.amber_file_parser as amber
receptor_system = amber.readAmberSystem(receptor_prmtop_filename, mm=openmm, gbmodel=gbmodel, nonbondedCutoff=None, nonbondedMethod='no-cutoff', shake='h-bonds')
complex_system = amber.readAmberSystem(complex_prmtop_filename, mm=openmm, gbmodel=gbmodel, nonbondedCutoff=None, nonbondedMethod='no-cutoff', shake='h-bonds')
ligand_system = amber.readAmberSystem(ligand_prmtop_filename, mm=openmm, gbmodel=gbmodel, nonbondedCutoff=None, nonbondedMethod='no-cutoff', shake='h-bonds')
coordinates = amber.readAmberCoordinates(complex_crd_filename)
# Create alchemically-modified system.
receptor_atoms = range(0,receptor_system.getNumParticles())
ligand_atoms = range(receptor_system.getNumParticles(), complex_system.getNumParticles())
valence_lambda = 1.0
coulomb_lambda = 0.0
vdw_lambda = 0.0
system = build_softcore_system(complex_system, receptor_atoms, ligand_atoms, valence_lambda, coulomb_lambda, vdw_lambda)
#system = build_custom_system(complex_system, receptor_atoms, ligand_atoms, valence_lambda, coulomb_lambda, vdw_lambda)
# Add harmonic potential.
kB = units.BOLTZMANN_CONSTANT_kB * units.AVOGADRO_CONSTANT_NA
kT = kB * temperature
beta = 1.0 / kT
gbmodel = 'OBC'
#gbmodel = None
# Load amber system.
receptor_prmtop_filename = 'receptor.prmtop'
complex_prmtop_filename = 'complex.prmtop'
ligand_prmtop_filename = 'ligand.prmtop'
complex_crd_filename = 'complex.crd'
import simtk.pyopenmm.amber.amber_file_parser as amber
receptor_system = amber.readAmberSystem(receptor_prmtop_filename,
mm=openmm,
gbmodel=gbmodel,
nonbondedCutoff=None,
nonbondedMethod='no-cutoff',
shake='h-bonds')
complex_system = amber.readAmberSystem(complex_prmtop_filename,
mm=openmm,
gbmodel=gbmodel,
nonbondedCutoff=None,
nonbondedMethod='no-cutoff',
shake='h-bonds')
ligand_system = amber.readAmberSystem(ligand_prmtop_filename,
mm=openmm,
gbmodel=gbmodel,
nonbondedCutoff=None,
nonbondedMethod='no-cutoff',
shake='h-bonds')
coordinates = amber.readAmberCoordinates(complex_crd_filename)
if __name__ == "__main__":
# Create system
system = openmm.System()
timestep = 1.0 * units.femtoseconds
# Set whether to use GB model or not.
gbmodel = 'OBC' # use OBC GBSA (gives finite error)
#gbmodel = 'none' # no solvent model (gives zero error)
# Load amber system for complex.
prmtop_filename = 'complex.prmtop'
crd_filename = 'complex.crd'
import simtk.pyopenmm.amber.amber_file_parser as amber
complex_system = amber.readAmberSystem(prmtop_filename, mm=openmm, gbmodel=gbmodel, shake='h-bonds')
complex_coordinates = amber.readAmberCoordinates(crd_filename)
# Load amber system for receptor only.
prmtop_filename = 'receptor.prmtop'
crd_filename = 'receptor.crd'
receptor_system = amber.readAmberSystem(prmtop_filename, mm=openmm, gbmodel=gbmodel, shake='h-bonds')
receptor_coordinates = amber.readAmberCoordinates(crd_filename)
# Create alchemically-modified system where ligand is turned off.
receptor_atoms = range(0,2603)
ligand_atoms = range(2603,2621)
alchemically_modified_complex_system = build_alchemically_modified_system(complex_system, receptor_atoms, ligand_atoms)
for platform_name in ['Cuda', 'Reference']:
# Select platform to use.