search

choderalab / openmoltools

An open set of tools for automating tasks relating to small molecules
MIT License
63 stars 30 forks source link

run_tleap raises exception running on Ambertools 19 #299

Open badisa opened 4 years ago

badisa commented 4 years ago

It appears that the version of tleap that comes with ambertools 19 (from conda) has added the following message when it exits Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0. which triggers the failure condition in check_command which looks for "Error" in every line as a failure case.

Moving to Ambertools 18.13 fixed this. Took a while to determine why as it seems that the log_debug_output flag doesn't provide any additional information in the scenario. Even if I set all loggers to debug.

The traceback:

03/07 21:16:01 [ForceField] Unexpected errors encountered running AMBER tool. Offending output:
03/07 21:16:01 [ForceField] Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
03/07 21:16:01 [ForceField] Failed to complete Error encountered running AMBER tool. Exiting.
03/07 21:16:01 [ForceField] Exception Error encountered running AMBER tool. Exiting. Apply Force Field
03/07 21:16:01 [ForceField] [ERROR] Traceback (most recent call last):
03/07 21:16:01 [ForceField]   File "/package/MDOrion/ForceField/cubes.py", line 202, in process
03/07 21:16:01 [ForceField]     excipient_structure = ffutils.applyffExcipients(excipients, opt)
03/07 21:16:01 [ForceField]   File "/package/MDOrion/ForceField/utils.py", line 337, in applyffExcipients
03/07 21:16:01 [ForceField]     ures_pmd = pmd.parameterize()
03/07 21:16:01 [ForceField]   File "/package/MDOrion/LigPrep/ff_utils.py", line 319, in parameterize
03/07 21:16:01 [ForceField]     structure = self.getGaffStructure()
03/07 21:16:01 [ForceField]   File "/package/MDOrion/LigPrep/ff_utils.py", line 284, in getGaffStructure
03/07 21:16:01 [ForceField]     leaprc="leaprc.%s" % forcefield.lower(),
03/07 21:16:01 [ForceField]   File "/home/floeuser/miniconda/envs/user_env/lib/python3.7/site-packages/openmoltools/amber.py", line 465, in run_tleap
03/07 21:16:01 [ForceField]     check_for_errors( output, other_errors = ['Improper number of arguments'] )
03/07 21:16:01 [ForceField]   File "/home/floeuser/miniconda/envs/user_env/lib/python3.7/site-packages/openmoltools/amber.py", line 257, in check_for_errors
03/07 21:16:01 [ForceField]     raise(RuntimeError("Error encountered running AMBER tool. Exiting."))
03/07 21:16:01 [ForceField] RuntimeError: Error encountered running AMBER tool. Exiting.