Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

leap returned non-zero exit status 31 #1309

Open
sobertie opened this issue Dec 11, 2023 · 0 comments
Open

leap returned non-zero exit status 31 #1309

sobertie opened this issue Dec 11, 2023 · 0 comments

Comments

@sobertie
Copy link

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 ?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant