leap returned non-zero exit status 31

[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: 300kelvin 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: 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]

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 ?