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leap returned non-zero exit status 31 #1309

@sobertie

Description

@sobertie

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: 300
kelvin
pressure: 1*atmosphere

molecules:
ft895:
filepath: ft895.mol2
antechamber:
charge_method: bcc
leap:
parameters: [leaprc.gaff]
hdac11:
filepath: input/hdac11.pdb

solvents:
water:
nonbonded_method: PME
nonbonded_cutoff: 9angstroms
clearance: 16
angstroms
solvent_model: tip4pew
leap:
parameters: [leaprc.water.tip4pew]
vacuum:
nonbonded_method: NoCutoff
buffer:
nonbonded_method: PME
nonbonded_cutoff: 11angstroms
clearance: 12
angstroms
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: 100
millimolar

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]

Whenever I run the script "yank script --yaml=yank_ft895.yaml"; following error occurs:
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 155, in dispatch
yaml_builder.run_experiments(write_status=write_status)
File "/home/mohon/anaconda3/envs/yank/lib/python3.9/site-packages/yank/experiment.py", line 737, in run_experiments
self._setup_experiments()
File "/home/mohon/anaconda3/envs/yank/lib/python3.9/site-packages/yank/experiment.py", line 2325, in _setup_experiments
self._db.setup_all_systems()
File "/home/mohon/anaconda3/envs/yank/lib/python3.9/site-packages/yank/pipeline.py", line 1395, in setup_all_systems
mpiplus.distribute(self.get_system,
File "/home/mohon/anaconda3/envs/yank/lib/python3.9/site-packages/mpiplus/mpiplus.py", line 523, in distribute
all_results = [task(job_args, *other_args, **kwargs) for job_args in distributed_args]
File "/home/mohon/anaconda3/envs/yank/lib/python3.9/site-packages/mpiplus/mpiplus.py", line 523, in
all_results = [task(job_args, *other_args, **kwargs) for job_args in distributed_args]
File "/home/mohon/anaconda3/envs/yank/lib/python3.9/site-packages/yank/pipeline.py", line 1346, in get_system
self._setup_system(system_files_paths[0].position_path,
File "/home/mohon/anaconda3/envs/yank/lib/python3.9/site-packages/yank/pipeline.py", line 1939, in _setup_system
warnings = tleap.run()
File "/home/mohon/anaconda3/envs/yank/lib/python3.9/site-packages/yank/utils.py", line 1702, in run
leap_output = subprocess.check_output(['tleap', '-f', 'leap.in']).decode()
File "/home/mohon/anaconda3/envs/yank/lib/python3.9/subprocess.py", line 424, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/home/mohon/anaconda3/envs/yank/lib/python3.9/subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['tleap', '-f', 'leap.in']' returned non-zero exit status 31.

How to circumvent this problem ?

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