[Chimera-users] inquire about molecular docking

[Elaine Meng]

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:
<http://vina.scripps.edu/>

The Chimera tool named “Autodock Vina” just connects to an outside web service that is running Autodock Vina.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> 

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
-----
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.