ModuleNotFoundError: No module named 'MolKit'

[JeongSooNa]

This error was encountered while running Tutorial, Preparing input data. How can we solve this?

(vina) root@3028709b6afa:/VINA/AutoDock-Vina/example/basic_docking/data# python /VINA/AutoDock-Vina/example/autodock_scripts/prepare_receptor.py -r 1iep_receptorH.pdb -o 1iep_receptorH.pdbqt Traceback (most recent call last): File "/VINA/AutoDock-Vina/example/autodock_scripts/prepare_receptor.py", line 9, in <module> from MolKit import Read ModuleNotFoundError: No module named 'MolKit'

(vina) root@3028709b6afa:/VINA/AutoDock-Vina/example/basic_docking/data# python /VINA/AutoDock-Vina/example/autodock_scripts/mk_prepare_ligand.py -i 1iep_ligand.sdf -o 1iep_ligand.pdbqt Traceback (most recent call last): File "/VINA/AutoDock-Vina/example/autodock_scripts/mk_prepare_ligand.py", line 9, in <module> from MolKit import Read

Ubuntu 20.04 Python 3.10.12

JeongSoo Na

[rwxayheee]

Hi @JeongSooNa, The 1st script uses MolKit as a dependency. Instead of using the environment python, try using ADFR's or mgltools's pythonsh to execute it. This script is no longer in this repository or the most recent release. But a similar one is: https://github.com/ccsb-scripps/AutoDock-Vina/blob/8604f73bf1f29b6f1ef4c4cdbbca0068e99d74fc/example/autodock_scripts/prepare_flexreceptor.py The usage is documented at the end of it.

A newer version of the 2nd script could be obtained from the Meeko project. As of today it doesn't seem to explicitly depend on MolKit.