unallowed value hdac11-ft895
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Hi everyone, I am estimating absolute free binding estimation of HDAC11 with its known ligand FT895.
Here is my yank_ft895.yaml file:
options:
verbose: yes
minimize: yes
default_timestep: 2.0femtoseconds
default_nsteps_per_iteration: 500
temperature: 300kelvin
pressure: 1*atmosphere
molecules:
ft895:
filepath: ft895.mol2
antechamber:
charge_method: bcc
leap:
parameters: [leaprc.gaff]
t4-lysozyme:
filepath: input/hdac11.pdb
solvents:
water:
nonbonded_method: PME
nonbonded_cutoff: 9angstroms
clearance: 16angstroms
solvent_model: tip4pew
leap:
parameters: [leaprc.water.tip4pew]
vacuum:
nonbonded_method: NoCutoff
buffer:
nonbonded_method: PME
nonbonded_cutoff: 11angstroms
clearance: 12angstroms
positive_ion: Na+
negative_ion: Cl-
ionic_strength: 100millimolar
solvent_model: tip3p
leap:
parameters: [leaprc.water.tip3p]
implicit:
nonbonded_method: NoCutoff
implicit_solvent: OBC2
implicit_solvent_salt_conc: 100millimolar
systems:
hydration-system:
solute: ft895
solvent1: water
solvent2: vacuum
leap:
parameters: [leaprc.protein.ff14SB]
hdac11-ft895:
receptor: hdac11
ligand: ft895
solvent: !Combinatorial [buffer, implicit]
leap:
parameters: [leaprc.protein.ff14SB, leaprc.water.tip4pew]
protocols:
hydration-protocol:
solvent1:
alchemical_path: auto
solvent2:
alchemical_path: auto
absolute-binding:
complex:
alchemical_path:
lambda_electrostatics: [1.00, 1.00, 1.00, 1.00, 1.00, 0.90, 0.80, 0.70, 0.60, 0.50, 0.40, 0.30, 0.20, 0.10, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00]
lambda_sterics: [1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 0.90, 0.80, 0.70, 0.60, 0.50, 0.40, 0.30, 0.20, 0.10, 0.00]
lambda_restraints: [0.00, 0.25, 0.50, 0.75, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00]
solvent:
alchemical_path: auto
experiment-hdac11-ft895:
system: hdac11-ft895
protocol: absolute-binding
restraint:
type: !Combinatorial [FlatBottom, Harmonic, Boresch]
experiment-hydration:
system: hydration-system
protocol: hydration-protocol
experiments: [experiment-hdac11-ft895, experiment-hydration]
But after running "yank script --yaml=yank_ft895.yaml" script I am getting the following error -
Traceback (most recent call last):
File "/home/mohon/anaconda3/envs/yank/bin/yank", line 10, in
sys.exit(main())
File "/home/mohon/anaconda3/envs/yank/lib/python3.9/site-packages/yank/cli.py", line 73, in main
dispatched = getattr(commands, command).dispatch(command_args)
File "/home/mohon/anaconda3/envs/yank/lib/python3.9/site-packages/yank/commands/script.py", line 147, in dispatch
yaml_builder = ExperimentBuilder(script=yaml_path, job_id=job_id, n_jobs=n_jobs)
File "/home/mohon/anaconda3/envs/yank/lib/python3.9/site-packages/yank/experiment.py", line 591, in init
self.parse(script)
File "/home/mohon/anaconda3/envs/yank/lib/python3.9/site-packages/yank/experiment.py", line 706, in parse
self._db.systems = self._validate_systems(yaml_content.get('systems', {}))
File "/home/mohon/anaconda3/envs/yank/lib/python3.9/site-packages/yank/experiment.py", line 1810, in _validate_systems
raise YamlParseError(error.format(system_id, yaml.dump(system_validator.errors)))
yank.experiment.YamlParseError: System 'hdac11-ft895_buffer' did not validate! Check the schema error below for details
receptor:
- unallowed value hdac11
How to circumvent this problem ?