[Chimera-users] inquire about molecular docking

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 30 12:51:00 PDT 2019

Hello Mohamed Hegazy,
Autodock Vina is a separate program (not inside Chimera) and you should check its website for more information about how it works:

The Chimera tool named “Autodock Vina” just connects to an outside web service that is running Autodock Vina.

This web service is a shared resource and does not allow very much sampling of space, and it only allows docking one small molecule at a time. Therefore, as mentioned in the help page linked above, we do not recommend using it for most research purposes. 

If you want to do better (more intensive) sampling of space, and/or dock a lot of small molecules to compare to each other, you should download Autodock Vina from the website above and run Autodock Vina directly.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 30, 2019, at 10:50 AM, Mohamed Hegazy <mohamedhegazy219427 at gmail.com> wrote:
> Hey ,
>           My name is Mohamed Hegazy, beginner in molecular docking  , recently I performed a molecular docking procedure using chimera and  I found that the initial structure of the ligand differs from the minimized one , and the binding score for a ligand would change during my different runs. The binding score you obtain from my docking cannot be a constant number. 

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