OSError: [Errno 39] Directory not empty

[Layne-Huang]

Hi,

It is really an excellent work. However, I have met some issues when running your code.

File "/nas-alinlp/lhuang/miniconda/envs/gbsa/lib/python3.10/shutil.py", line 729, in rmtree
    os.rmdir(path)
OSError: [Errno 39] Directory not empty: '/ligand_file_name/UNIGBSA'

Could you please tell me how to solve it?

[Aunity]

Hi, this is a bug of uni-gbsa. You could ignore this bug by add the --verbose paras.

[Layne-Huang]

Maybe there is another bug. When I ran unigbsa-pipeline, it will throw out:

os.chdir(f'{molname}.acpype')
FileNotFoundError: [Errno 2] No such file or directory: 'MOL.acpype'

However, it successfully ran when I rerun the unigbsa-pipeline.

05/31/2023 20:48:42 PM - INFO - Build protein topology.
05/31/2023 20:48:44 PM - INFO - Build ligand topology: 7l11_4747
05/31/2023 20:49:07 PM - INFO - Running energy minimization: 7l11_4747
05/31/2023 20:49:13 PM - INFO - Run the MMPB(GB)SA.
05/31/2023 20:49:27 PM - INFO - Clean the results.
================================================================================
Results: Energy.csv Dec.csv
Frames    mode    detal_G(kcal/mole)
     1      gb              -56.8643  

[Layne-Huang]

Besides, it always throw out error when building protein topology:

raise Exception('ERROR run gmx! see the log file for details %s'%os.path.abspath("gromacs.log"))
Exception: ERROR run gmx! see the log file for details

It also throws out errors when building ligand topology:

Traceback (most recent call last):
  File "/miniconda/envs/gbsa/lib/python3.10/site-packages/acpype/cli.py", line 140, in init_main
    molecule.createMolTopol()
  File "/miniconda/envs/gbsa/lib/python3.10/site-packages/acpype/topol.py", line 1116, in createMolTopol
    self.topFileData = open(self.acTopFileName).readlines()
FileNotFoundError: [Errno 2] No such file or directory: 'MOL_AC.prmtop'
Total time of execution: 8s

[Aunity]

Could you please upload your ligand and protein files? It seems like your ligand do not prepare well.