promoted_name='protein_ff',
default='amber99sbildn.xml')
ff.promote_parameter('solvent_forcefield',
promoted_name='solvent_ff',
default='tip3p.xml')
ff.promote_parameter('ligand_forcefield',
promoted_name='ligand_ff',
default='GAFF2')
ff.promote_parameter('other_forcefield',
promoted_name='other_ff',
default='GAFF2')
# Output the prepared systems
complex_prep_ofs = OEMolOStreamCube('complex_prep_ofs',
title='ComplexSetUpOut')
complex_prep_ofs.set_parameters(backend='s3')
complex_prep_ofs.set_parameters(
data_out=iprot.promoted_parameters['protein_prefix']['default'] +
'_SetUp.oeb.gz')
# Minimization
minComplex = OpenMMminimizeCube('minComplex', title='Minimize')
minComplex.promote_parameter('restraints',
promoted_name='m_restraints',
default="noh (ligand or protein)",
description='Select mask to apply restarints')
minComplex.promote_parameter('restraintWt',
promoted_name='m_restraintWt',
default=5.0,
description='Restraint weight')
minComplex.promote_parameter('steps', promoted_name='steps', default=20000)
nvt = OpenMMnvtCube('nvt')
nvt.promote_parameter('time', promoted_name='picosec', default=10.0)
nvt.promote_parameter('temperature', promoted_name='temperature', default=300.0,
description='Selected temperature in K')
# Restraints
nvt.promote_parameter('restraints', promoted_name='restraints', default='noh (ligand or protein)')
nvt.promote_parameter('restraintWt', promoted_name='restraintWt', default=2.0)
# Trajectory and logging info frequency intervals
nvt.promote_parameter('trajectory_interval', promoted_name='trajectory_interval', default=100,
description='Trajectory saving interval')
nvt.promote_parameter('reporter_interval', promoted_name='reporter_interval', default=1000,
description='Reporter saving interval')
nvt.promote_parameter('outfname', promoted_name='suffix', default='nvt',
description='Equilibration suffix name')
ofs = OEMolOStreamCube('ofs', title='OFS-Success')
ofs.set_parameters(backend='s3')
fail = OEMolOStreamCube('fail', title='OFS-Failure')
fail.set_parameters(backend='s3')
fail.set_parameters(data_out='fail.oeb.gz')
job.add_cubes(ifs, nvt, ofs, fail)
ifs.success.connect(nvt.intake)
nvt.success.connect(ofs.intake)
nvt.failure.connect(fail.intake)
if __name__ == "__main__":
job.run()
job.description = """
**Check available OpenMM Platforms**
Based on OpenMM SimTK installation check script
"""
job.classification = [
["OpenMM", "Platforms"]
]
job.tags = [tag for lists in job.classification for tag in lists]
ifs = OEMolIStreamCube("ifs")
ofs = OEMolOStreamCube("ofs")
# Promotes the parameter to something we can specify from the command line as "--ifs=..."
ifs.promote_parameter("data_in", promoted_name="ifs")
# this is hardwiring the filename to the molecules coming out of ofs
ofs.set_parameters(data_out="openmmPlatformCheck.oeb")
# the name of the object has to match the string: this is the name of myself
platformTester = PlatformTestCube("platformTester")
job.add_cubes(ifs, ofs, platformTester)
ifs.success.connect(platformTester.intake)
platformTester.success.connect(ofs.intake)
if __name__ == "__main__":
job.run()