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pharmai / plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

Home Page:http://plip.biotec.tu-dresden.de

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How to go about finding interacting Amino Acid Residues of ~1 billion compounds (In PDBQT)

eschoo opened this issue · comments

commented

Hi,

I was recently introduced to PLIP in order to find all interacting Amino Acid residues between a protein and a ligand (PDBQT files that are within .tar collections). I ran these docking through HPC Cluster. I have Singularity activated in the Cluster but when I ran the $ ./plip.simg -i 1vsn -yv command, it returned with No such file or directory error.

I then tried installing it to the Cluster through the Source from the Documentation. After installation and simplifying the access to PLIP, whenever I use the plip command, I get an error of:

File "/home/usr/plip/plip/plipcmd.py", line 28
description = f"The Protein-Ligand Interaction Profiler (PLIP) Version {version} "
^
SyntaxError: invalid syntax

I would really appreciate help for making a progress with my project! Thanks!

commented

Please use a subject line shortly describing the issue, in this case a better one would be for example "Can not run plip on HPC environment" or similar.

For the first issue, please verify that the singularity image file is actually executable or try to call the singularity command explicitly: singularity run <path_to_plip.simg>

The shebang of plipcmd is #! /usr/bin/env python so it picks up whatever python you have in your $PATH, make sure it is Python3 >= 3.6.9 and not python2 for example.