yank
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Published
20 hours ago •
choderalab
choderalab
Setting problem during absolute binding energy calculation (maybe in complex phase...?)
When I run the absolute calculation protocol, I got the error below
/home/juyong/apps/amber18/bin:/home/juyong/anaconda3/envs/yank/bin:/usr/local/cuda-10.1/bin:/appl/anaconda3/envs/openmm_env/bin:/appl/mpi/intel/openmpi-4.0.2/bin:/usr/local/cuda-10.1/bin/:/opt/intel/advisor_2017.1.5.527008/bin64:/opt/intel/vtune_amplifier_xe_2017.6.0.554757/bin64:/opt/intel/inspector_2017.1.4.527006/bin64:/opt/intel/itac/2019.5.041/intel64/bin:/opt/intel//itac/2019.5.041/intel64/bin:/opt/intel//clck/2019.5/bin/intel64:/opt/intel/compilers_and_libraries_2019.5.281/linux/bin/intel64:/opt/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/bin:/opt/intel/debugger_2019/gdb/intel64_mic/bin:/opt/gromacs-2019.4-plumed/bin:/home/byun/anaconda3/bin:/home/byun/anaconda3/condabin:/home/juyong/apps/amber18/bin:/opt/mmpbsa/bin:/opt/APBS-1.4/bin:/opt/plumed-2.5.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/home/juyong/apps/amber18/bin:/home/choi/docking/ucsf/dock6/bin:/home/byun/apps/GalaxyDock3/bin:/home/byun/.local/bin:/home/byun/bin:/opt/intel/parallel_studio_xe_2017.8.066/bin
/home/juyong/anaconda3/envs/yank/bin/mpirun
2020-10-12 16:54:25,297: Setting CUDA platform to use precision model 'double'.
2020-10-12 16:54:25,396: WARNING - openmmtools.multistate.multistatesampler - Warning: The openmmtools.multistate API is experimental and may change in future releases
2020-10-12 16:54:25,396: WARNING - openmmtools.multistate.multistatesampler - Warning: The openmmtools.multistate API is experimental and may change in future releases
2020-10-12 16:54:25,425: Node 1/2: executing <function ExperimentBuilder._check_resume at 0x7f5bcc4fe200>
2020-10-12 16:54:25,429: Node 1/2: waiting for barrier after <function ExperimentBuilder._check_resume at 0x7f5bcc4fe200>
2020-10-12 16:54:25,433: Node 1/2: waiting for barrier after _setup_molecules
2020-10-12 16:54:25,434: Group 1/2 Node 1/1: execute get_system(complex)
2020-10-12 16:54:25,434: Setting up the systems for Tubulin and LIG using solvent pme
2020-10-12 16:54:25,434: Setting up solvent phase
2020-10-12 16:54:25,935: Setting up complex phase
Traceback (most recent call last):
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/mpiplus/mpiplus.py", line 357, in exec_tasks
results.append(task(distributed_arg, *other_args, **kwargs))
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/yank/pipeline.py", line 1349, in get_system
ligand_id)
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/yank/pipeline.py", line 1939, in _setup_system
warnings = tleap.run()
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/yank/utils.py", line 1702, in run
leap_output = subprocess.check_output(['tleap', '-f', 'leap.in']).decode()
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/subprocess.py", line 411, in check_output
**kwargs).stdout
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/subprocess.py", line 512, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['tleap', '-f', 'leap.in']' returned non-zero exit status 31.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/juyong/anaconda3/envs/yank/bin/yank", line 11, in <module>
load_entry_point('yank==0.25.2', 'console_scripts', 'yank')()
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/yank/cli.py", line 73, in main
dispatched = getattr(commands, command).dispatch(command_args)
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/yank/commands/script.py", line 155, in dispatch
yaml_builder.run_experiments(write_status=write_status)
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/yank/experiment.py", line 737, in run_experiments
self._setup_experiments()
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/yank/experiment.py", line 2325, in _setup_experiments
self._db.setup_all_systems()
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/yank/pipeline.py", line 1397, in setup_all_systems
send_results_to=None, group_size=1, sync_nodes=True)
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/mpiplus/mpiplus.py", line 531, in distribute
*other_args, **kwargs)
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/mpiplus/mpiplus.py", line 360, in exec_tasks
error = type(e)('{}: {}'.format(node_name, str(e)))
TypeError: __init__() missing 1 required positional argument: 'cmd'
2020-10-12 17:08:08,901: CRITICAL - mpiplus.mpiplus - MPI node 1/2 raised an exception and called Abort()! The exception traceback follows
Traceback (most recent call last):
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/mpiplus/mpiplus.py", line 357, in exec_tasks
results.append(task(distributed_arg, *other_args, **kwargs))
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/yank/pipeline.py", line 1349, in get_system
ligand_id)
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/yank/pipeline.py", line 1939, in _setup_system
warnings = tleap.run()
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/yank/utils.py", line 1702, in run
leap_output = subprocess.check_output(['tleap', '-f', 'leap.in']).decode()
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/subprocess.py", line 411, in check_output
**kwargs).stdout
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/subprocess.py", line 512, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['tleap', '-f', 'leap.in']' returned non-zero exit status 31.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/juyong/anaconda3/envs/yank/bin/yank", line 11, in <module>
load_entry_point('yank==0.25.2', 'console_scripts', 'yank')()
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/yank/cli.py", line 73, in main
dispatched = getattr(commands, command).dispatch(command_args)
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/yank/commands/script.py", line 155, in dispatch
yaml_builder.run_experiments(write_status=write_status)
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/yank/experiment.py", line 737, in run_experiments
self._setup_experiments()
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/yank/experiment.py", line 2325, in _setup_experiments
self._db.setup_all_systems()
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/yank/pipeline.py", line 1397, in setup_all_systems
send_results_to=None, group_size=1, sync_nodes=True)
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/mpiplus/mpiplus.py", line 531, in distribute
*other_args, **kwargs)
File "/home/juyong/anaconda3/envs/yank/lib/python3.7/site-packages/mpiplus/mpiplus.py", line 360, in exec_tasks
error = type(e)('{}: {}'.format(node_name, str(e)))
TypeError: __init__() missing 1 required positional argument: 'cmd'
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
I think that the subprocess error related to the tleap might be from the amber tleap. But when I uesd the tleap directly, there was no problem....
Could you tell me what I am missing... Thank you:)
Below is the my yaml input file
---
options:
minimize: yes
verbose: yes
temperature: 300 * kelvin
pressure: 1 * atmosphere
output_dir: double
precision: double
platform: CUDA
resume_setup: yes
resume_simulation: yes
default_timestep: 2.0 * femtoseconds
default_nsteps_per_iteration: 500
default_number_of_iterations: 5000
number_of_equilibration_iterations: 100
equilibration_timestep: 1.0 * femtosecond
molecules:
Tubulin:
filepath: Cor_Tubulin_.pdb
LIG:
filepath: ./INPUT/LIG/drawing_3D.mol2
antechamber:
charge_method: bcc
solvents:
pme:
nonbonded_method: PME
switch_distance: 11*angstroms
nonbonded_cutoff: 12*angstroms
ewald_error_tolerance: 1.0e-4
clearance: 9*angstroms
positive_ion: Na+
negative_ion: Cl-
systems:
complex:
receptor: Tubulin
ligand: LIG
solvent: pme
leap:
parameters: [leaprc.protein.ff14SB, leaprc.gaff, leaprc.water.tip4pew, INPUT/LIG/lig.frcmod, INPUT/GDP/gdp.frcmod, INPUT/GTP/gtp.frcmod ]
samplers:
replica-exchange:
type: ReplicaExchangeSampler
replica_mixing_scheme: swap-all
online_analysis_interval: 100
online_analysis_target_error: 3.0
online_analysis_minimum_iterations: 50
protocols:
absolute-binding:
complex:
alchemical_path:
lambda_restraints: [0.00, 0.05, 0.10, 0.15, 0.20, 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, 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, 1.000, 1.00, 1.000, 1.00, 1.00]
lambda_electrostatics: [1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.05, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.000, 0.00, 0.000, 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, 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, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.075, 0.05, 0.025, 0.01, 0.00]
solvent:
alchemical_path:
lambda_electrostatics: [1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.05, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 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, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.00]
experiments:
system: complex
protocol: absolute-binding
restraint:
type: Boresch
I generated the .frcmod files from the amber antechamber and parmchk2
Hi @Byun-jinyoung . Yes, that looks like a leap error. Which leap command and script are you using to try to reproduce the error? Is the leap script you are testing similar to what you (should) find in the system folder?
