autodockvina

Question

[iamsmor]

Hi everyone,

I am trying to do docking by python script and for this I using to prepare-receptor4.py but it gives many error because of I am using python3, I tried to fixed script but at the end of trying I got error

from MolKit import Read
ModuleNotFoundError: No module named 'MolKit'

and I edited it as

#!/usr/bin/env python
from AutoDockTools.MoleculeTools import Read
from AutoDockTools.MoleculeTools import Mol
from AutoDockTools.MoleculeTools import Protein
from AutoDockTools.MoleculePreparation import AD4ReceptorPreparation

and I get error again

from AutoDockTools.MoleculeTools import Read
ModuleNotFoundError: No module named 'AutoDockTools'

Can anyone help me how I can use this script for python3 or anyone else having this problem

Thank you

[zorbax]

Hi, you need to provide more information. What kind of "docking by Python scripts" are you trying to use? Which version of AutoDockTools is using because now it is provided as part of MGLTools? Did you use Conda to install it? Which OS are you working with?

[iamsmor]

ı use ubuntu 20.04 and ı have installed AutoDock 4.2.6 . ı have a ligand and ı will dock it with as many possible proteins.I am trying do set pipeline for my work as prepare pdbqt by commend and later do blind docking. First ı tried to do on my terminale but it gives conflict because of ı have python3 and mgtools prepared_receptor4.py for python2 so at last ı am triying to do on shell of mgltools but it still unprogressive :(