I am using 4.2.6 version but new version is preferred.

try always to update to latest version, that would help you to include more force field parameters to your docking environment

I think it is better you try AutoDock Vina software. Molecular docking with Vina needs less time and its results are more accurate.

Dear Oraas Adnan Hatem,

I would recommend Autodock/Vina plugin - Pymol because it is easy to use and great tool for docking analysis.

Kindly find the source link and video tutorial

http://wwwuser.gwdg.de/~dseelig/adplugin.html

http://wwwuser.gwdg.de/~dseelig/plugin_tutorial.html

Cheers

AutoDock4 and Autodock Vina are different programs. Both the scoring function and the search algorithm are dissimilar. AutoDock4 (4.2.6) is generally used for binding mode prediction and Vina for virtual screening. Vina is faster and has somewhat easier input preparation.

AutoDock Vina is the best software but can be a bit tricky sometime, especially if you make mistakes while preparing the protein and ligand. Also if you are looking to dock modelled structure then, the process is bit different than what you use while docking with a structure from PDB

You can use Pyrex. It will help you to screen multiple compounds at a time and work via autodock environment.

AutoDock Vina is the best.

If you want to do further research in vitro, I suggest using AutoDock 4