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Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
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error when running gmx_MMPBSA_test #130

Closed wangjiaqi8710 closed 2 years ago

wangjiaqi8710 commented 2 years ago

Hello Sir,

I have encountered the below error when I try to run gmx_MMPBSA_test. Could you suggest a way to fix it? I used ubuntu 18.04 and have python3.6.9 installed in the system.

The error message is

"FileNotFoundError: [Errno 2] No such file or directory: 'gmx_MMPBSA_test/docs/examples/Protein_DNA_RNA_Ion_ligand/README.md'"

The full output is shown below

$ gmx_MMPBSA_test Error processing line 1 of /home/amber20/miniconda/lib/python3.9/site-packages/distutils-precedence.pth:

Traceback (most recent call last): File "/home/amber20/miniconda/lib/python3.9/site.py", line 169, in addpackage exec(line) File "", line 1, in ModuleNotFoundError: No module named '_distutils_hack'

Remainder of file ignored [INFO ] Cloning gmx_MMPBSA repository in gmx_MMPBSA_test Cloning into 'gmx_MMPBSA_test'... remote: Enumerating objects: 10527, done. remote: Counting objects: 100% (1233/1233), done. remote: Compressing objects: 100% (299/299), done. remote: Total 10527 (delta 848), reused 1100 (delta 735), pack-reused 9294 Receiving objects: 100% (10527/10527), 262.32 MiB | 2.71 MiB/s, done. Resolving deltas: 100% (7454/7454), done. Checking out files: 100% (456/456), done. [INFO ] Cloning gmx_MMPBSA repository...Done. Traceback (most recent call last): File "/home/amber20/miniconda/bin/gmx_MMPBSA_test", line 8, in sys.exit(gmxmmpbsa_test()) File "/home/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 146, in gmxmmpbsa_test run_test(parser) File "/home/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/tester.py", line 110, in run_test with open(test[x][0].joinpath('README.md')) as readme: FileNotFoundError: [Errno 2] No such file or directory: 'gmx_MMPBSA_test/docs/examples/Protein_DNA_RNA_Ion_ligand/README.md'

Thank you for your help.

Jiaqi wang

Describe the issue A clear and concise description of what the issue is.

If you will report an error, please complete this form To Reproduce Steps to reproduce the behavior:

  1. Which system type are you running? (Protein-Protein, Protein-Ligand, etc)
  2. The command-line are you using.

Additional context The gmx_MMPBSA.log file

Valdes-Tresanco-MS commented 2 years ago

In the current version of the program (v1.4.3), it is a reported bug (See issue #46). It is solved by specifying the path where the folder will be created using the -f option explicitly. This error has already been fixed for the version v1.5.0 that is coming out soon

wangjiaqi8710 commented 2 years ago

In the current version of the program (v1.4.3), it is a reported bug (See issue #46). It is solved by specifying the path where the folder will be created using the -f option explicitly. This error has already been fixed for the version v1.5.0 that is coming out soon

may I know in which step should I specify the path? I currently install it based on what is suggested in this link https://valdes-tresanco-ms.github.io/gmx_MMPBSA/installation/.

$amber.python -m pip install PyQt5 $amber.python -m pip install gmx_MMPBSA

Am I doing it right?

Thanks for reply. JQ

Valdes-Tresanco-MS commented 2 years ago

The error you get when running gmx_MMPBSA_test has been previously reported (See issue #46). To solve it you must explicitly define the address of the test folder with the -f option, for example, gmx_MMPBSA_test -f /home/mario/Documents. A folder called gmx_MMPBSA_test will be created at that address.