[Chimera-users] Issue regarding Chimera-Vina

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 11 09:17:49 PDT 2019

Dear Prabuddha Bhattacharya,
Autodock Vina is not part of Chimera - instead the Chimera tool just sends your structures to a web service somewhere else that is running Autodock Vina, and then shows you the results that come back.

Our group does not develop Autodock Vina, nor do we run this web service.  All I can say is to look at the Autodock Vina website and paper to understand how it works.

Another important thing to note about the web service is that as a public/shared resource, it only allows a small amount of sampling for one ligand at a time.  It is not recommended for comparing many ligands, and even for one ligand, the sampling may not be enough for most research projects.  For most research cases, it would be better to download Autodock Vina from its website and to use it directly (not from Chimera).
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 10, 2019, at 9:31 PM, Prabuddha Bhattacharya <b.prabuddha3 at gmail.com> wrote:
> Dear Sir,
> I am a beginner in  the field of molecular docking. However, I started doing it using Chimera Vina. UCSF Chimera 1.13rc provides the interface while AutoDock Vina does the docking part.
> For a couple of cases I have found that inspite of keeping all the parameters same, the best obtained dock scores are coming different for each individual job-run. Is it so because it is a stocastic method? With such different dock scores, what should I do?
> I will be extremely grateful of you can kindly address this issue.
> Thanking you in advance,
> Best regards
> -- 
> Prabuddha Bhattacharya 

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