Dear all,
I have troubles setting my Autodock Vina plugin in Pymol 2.3.4 at Windows10 and also at my virtual machine with Ubuntu. When I want to generate receptor it has problem with prepare_receptor4.py script (same with ligand script) that is written in python2 and Pymol interprets it in python3 I gues. I am able to use this script alone to generate .pdbqt files when I create new enviroment in Anaconda in python2.7... but still cant use Pymol plugin. I tried to convert these scripts to Py3 using 2to3 command but I gues the whole plugin is in Py2 becouse it gave me an error that could not find MolKit module. Any ideas? Or downloading old Pymol is the only option?
Aleksandar thank you for your response. I have two problems... first, at windows I am trying to run scripts from MGLtools for ligand/receptor preparing (prepare_ligand4.py) for docking. I am running them in python 2 enviroment created in Anaconda. But these scripts can't find modules from MGLtools (specifically MolKit module) eventhough I tried to add path to these modules to PYTHONPATH, or just copy them to site-packages in python file location (python is in my PATH variable). Hence I downloaded virtualbox and installed ubutnu, where you can install MGLtools directly to anaconda modules (not avalaible in windows). Thanks to this I can run scripts for ligand/receptor preparing in python2 enviroment where I also instaled MGLtools. But here comes the second problem - when I am trying to run Autodock Vina plugin in PyMol with interactive gui (this plugin is using MGLtools and same scripts for preparing ligands and receptors) it gives me error, becouse it interprets these scripts in python3 - PyMol has it's own python3 interpreter.
Mohammed thank you for advice, I am already using virtual enviroments with different python versions
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