ligid = IDSettingCube("Ligand Ids")
# Protein Reading cube. The protein prefix parameter is used to select a name for the
# output system files
iprot = DatasetReaderCube("ProteinReader", title="Protein Reader")
iprot.promote_parameter("data_in",
promoted_name="protein",
title='Protein Input Dataset',
description="Protein Dataset")
# Complex cube used to assemble the ligands and the solvated protein
complx = ComplexPrepCube("Complex", title="Complex Preparation")
complx.set_parameters(lig_res_name='LIG')
# Protein Setting
protset = MDComponentCube("ProteinSetting", title="Protein Setting")
ofs = DatasetWriterCube('ofs', title='MD Out')
ofs.promote_parameter("data_out",
promoted_name="out",
title="MD Out",
description="MD Dataset out")
fail = DatasetWriterCube('fail', title='Failures')
fail.promote_parameter("data_out",
promoted_name="fail",
title="Failures",
description="MD Dataset Failures out")
job.add_cubes(iligs, ligset, ligid, iprot, protset, chargelig, complx, ofs,
fail)
solvate = ParallelSolvationCube("Solvation", title="Solvation")
solvate.set_parameters(density=1.03)
solvate.set_parameters(salt_concentration=50.0)
# solvate.set_parameters(close_solvent=True)
solvate.modify_parameter(solvate.close_solvent, promoted=False, default=False)
# Force Field Application
ff = ParallelForceFieldCube("ForceField", title="Apply Force Field")
ff.promote_parameter('protein_forcefield',
promoted_name='protein_ff',
default='Amber99SBildn')
ff.promote_parameter('ligand_forcefield',
promoted_name='ligand_ff',
default='Gaff2')
mdcomp = MDComponentCube("MDComponentSetting", title="MDComponentSetting")
# mdcomp.promote_parameter("flask_title", promoted_name="flask_title", default='MCL1')
ofs = DatasetWriterCube('ofs', title='MD Out')
ofs.promote_parameter("data_out",
promoted_name="out",
title="MD Out",
description="MD Dataset out")
fail = DatasetWriterCube('fail', title='Failures')
fail.promote_parameter("data_out",
promoted_name="fail",
title="Failures",
description="MD Dataset Failures out")
job.add_cubes(iligs, chargelig, ligset, ligid, iprot, mdcomp, complx, solvate,
# This Cube is necessary for the correct work of collection and shard
coll_open = CollectionSetting("OpenCollection", title="Open Collection")
coll_open.set_parameters(open=True)
# Force Field Application
ff = ParallelForceFieldCube("ForceField", title="Apply Force Field")
ff.promote_parameter('protein_forcefield',
promoted_name='protein_ff',
default='Amber14SB')
ff.promote_parameter('ligand_forcefield',
promoted_name='ligand_ff',
default='OpenFF_1.3.0')
# Protein Setting
mdcomp = MDComponentCube("MD Components", title="MD Components")
mdcomp.promote_parameter("flask_title",
promoted_name="flask_title",
default="")
# Production run
prod = ParallelMDNptCube("Production", title="Production")
prod.promote_parameter('time',
promoted_name='prod_ns',
default=2.0,
description='Length of MD run in nanoseconds')
prod.promote_parameter('trajectory_interval',
promoted_name='prod_trajectory_interval',
default=0.004,
description='Trajectory saving interval in ns')
prod.promote_parameter(
iprot.promote_parameter("data_in", promoted_name="protein", title="Protein Input File", description="Protein file name")
complx = ComplexPrepCube("Complex")
solvate = ParallelSolvationCube("Hydration", title='System Hydration')
solvate.promote_parameter('density', promoted_name='density', default=1.03,
description="Solution density in g/ml")
solvate.promote_parameter('salt_concentration', promoted_name='salt_concentration', default=50.0,
description='Salt concentration (Na+, Cl-) in millimolar')
solvate.set_parameters(close_solvent=True)
ff = ParallelForceFieldCube("ForceField", title="System Parametrization")
ff.promote_parameter('protein_forcefield', promoted_name='protein_ff', default='Amber99SBildn')
ff.promote_parameter('ligand_forcefield', promoted_name='ligand_ff', default='Gaff2')
mdcomp = MDComponentCube("MDComponentSetting", title="MDComponentSetting")
mdcomp.promote_parameter("flask_title", promoted_name="slack_title", default="")
# Minimization
minimize = ParallelMDMinimizeCube('minComplex', title="System Minimization")
minimize.promote_parameter('steps', promoted_name='steps', default=2000)
minimize.promote_parameter('md_engine', promoted_name='md_engine', default='OpenMM',
description='Select the MD Engine')
ofs = DatasetWriterCube('ofs', title='Out')
ofs.promote_parameter("data_out", promoted_name="out")
fail = DatasetWriterCube('fail', title='Failures')
fail.promote_parameter("data_out", promoted_name="fail")
job.add_cubes(iligs, chargelig, ligset, ligid,
job.description = open(path.join(path.dirname(__file__), 'PlainMD_desc.rst'), 'r').read()
# Locally the floe can be invoked by running the terminal command:
# python floes/PlainMD.py --ligands ligands.oeb --protein protein.oeb --out prod.oeb
job.classification = [['General MD']]
job.uuid = "266481fc-b257-41e9-b2f9-a92bf028b701"
job.tags = [tag for lists in job.classification for tag in lists]
ifs = DatasetReaderCube("SystemReader", title="System Reader")
ifs.promote_parameter("data_in", promoted_name="solute", title='Solute Input File',
description="Solute input file")
sysid = IDSettingCube("System Ids")
md_comp = MDComponentCube("MD Components")
md_comp.set_parameters(multiple_flasks=True)
# The solvation cube is used to solvate the system and define the ionic strength of the solution
solvate = ParallelSolvationCube("Hydration", title="Hydration")
solvate.promote_parameter('density', promoted_name='density', default=1.03,
description="Solution density in g/ml")
solvate.promote_parameter('salt_concentration', promoted_name='salt_concentration', default=50.0,
description='Salt concentration (Na+, Cl-) in millimolar')
solvate.set_parameters(close_solvent=True)
# This Cube is necessary for the correct work of collection and shard
coll_open = CollectionSetting("OpenCollection", title="Open Collection")
coll_open.set_parameters(open=True)