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issues with docking result

Posted: Tue Dec 14, 2021 12:06 pm
by koesuki123
Hello. I accidentally prepared and docked two files of same ligand. I use Avogadro to optimize both of these ligands files. However, the docking result (on same protein) indicated that both of these ligands had different binding energies and poses.

So I want to ask if it is normal to have different result although it is the same ligand? Or there is actually something wrong with my AutoDock Vina software? Anyone can comment on docking result reproducibility?

Asking for help! Thank you!

Re: issues with docking result

Posted: Tue Dec 14, 2021 1:01 pm
by xiaogenz
It is possible to obtain different docking poses for the same receptor and ligand when you run several times for docking programs.
The initial docking poses are different because the program starts from randomly translating the ligand into the binding pocket, then does simulation to find the docking pose with the best score.
So, the binding energy will also be different for the final results.