MMPBSA/MMGBSA tool-help

usegalaxy.eu support
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1

How to sort this error?

              File "/usr/local/tools/_conda/envs/mulled-v1-1da566b6d6a079490cb40294aceebefb88269cd589e067c0fa7206262108fbce/bin/MMPBSA.py", line 99, in <module>
    app.file_setup()
  File "/usr/local/tools/_conda/envs/mulled-v1-1da566b6d6a079490cb40294aceebefb88269cd589e067c0fa7206262108fbce/lib/python3.9/site-packages/MMPBSA_mods/main.py", line 155, in file_setup
    self.numframes, self.numframes_nmode = make_trajectories(INPUT, FILES,
  File "/usr/local/tools/_conda/envs/mulled-v1-1da566b6d6a079490cb40294aceebefb88269cd589e067c0fa7206262108fbce/lib/python3.9/site-packages/MMPBSA_mods/make_trajs.py", line 104, in make_trajectories
    traj.Strip(INPUT['ligand_mask'])
  File "/usr/local/tools/_conda/envs/mulled-v1-1da566b6d6a079490cb40294aceebefb88269cd589e067c0fa7206262108fbce/lib/python3.9/site-packages/MMPBSA_mods/make_trajs.py", line 646, in Strip
    raise InternalError('Cannot pass no mask to Strip!')
InternalError: Cannot pass no mask to Strip!

Fatal Error! 
All files have been retained for your error investigation: 
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.
2

Welcome @swathin

The error is reporting a data issue. There is probably a format problem with the input ligand file, or possibly the terms used for the Strip mask parameter on the form. We can’t see those details yet.

The instruction on the form list out the preparation steps. Doing this in Galaxy would be recommended to avoid technical formatting conflicts. So, if you did this somewhere else and uploaded the inputs to this tool, redoing those steps is one suggestion to try.

If you would like more help, we would need a few more details about your specific job please. You can do this by generating a history share link and pasting it back here for feedback. Thanks! :slight_smile: