Is it possible to run gmx_MMPBSA_ana as a standalone?

[Ludovico Pipitò]

Good evening!

I have really appreciated the efforts put into gmx_MMPBSA!

I have some previously made GBSA elaborations, and I wondered if I could use the plotting tool, which looks great especially for DECOMP analysis.

Unfortunately, when I input:

"gmx_MMPBSA_ana -f 1GBSA_ALL_results_mmpbsa.dat" or "gmx_MMPBSA_ana -f _MMPBSA_info" I get the following error:

Traceback (most recent call last):
  File "/home/pipitoludovico/miniconda3/bin/gmx_MMPBSA_ana", line 8, in <module>
    sys.exit(gmxmmpbsa_ana())
  File "/home/pipitoludovico/miniconda3/lib/python3.7/site-packages/GMXMMPBSA/app.py", line 129, in gmxmmpbsa_ana
    w.initialize(ifiles)
  File "/home/pipitoludovico/miniconda3/lib/python3.7/site-packages/GMXMMPBSA/analyzer/gui.py", line 317, in initialize
    self.init_dialog.get_files_info(info_files)
  File "/home/pipitoludovico/miniconda3/lib/python3.7/site-packages/GMXMMPBSA/analyzer/dialogs.py", line 214, in get_files_info
    item = QTreeWidgetItem([f'{fname.parent.name}', '', f'{basename}', f'{exp_ki}', f'{temp}',
UnboundLocalError: local variable 'temp' referenced before assignment

I wonder if I am missing something.

The .log file just reports:

[INFO   ] Starting

The test runs fine until the alanine scanning.

Thanks!

Ludovico

[Mario Sergio Valdes]

Hello and welcome.
Thank you very much for appreciating the effort.
Are your results from calculations made with gmx_MMPBSA or with another program? gmx_MMPBSA_ana works as a stand-alone program, but only for output from gmx_MMPBSA. You can check the details here (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/command-line/#gmx_mmpbsa_ana-command-line) and here (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/analyzer/).
We are currently working on implementing MMPBSA.py for Amber users, however, this will be available for version 2.0.0. The current development version (1.5.0), soon to be released, will have significant improvements in the three tools (gmx_MMPBSA, gmx_MMPBSA_ana, and gmx_MMPBSA_test), but it will be incompatible with the previous ones.
We hope you can use gmx_MMPBSA in your research

Sincerely

Mario S.

[Ludovico Pipitò]

Thank you for your reply!

Yes, I have used MMPBSA.py to get the calculations and the DECOMP analysis, and this might be the reason why this error happens.

Thank you for this beautiful tool!

All the best,

Ludovico