[Chimera-users] How to setup appropriate parameters during auto dock vina

Elaine Meng meng at cgl.ucsf.edu
Sat Mar 2 09:26:01 PST 2019

Autodock Vina is a separate program (not inside Chimera) and you should check its website and the information there:

The Chimera tool named “Autodock Vina” just connects to an outside web service that is running Autodock Vina.  Because it is a shared resource, this web service does not allow very much sampling of space, and it only allows docking one small molecule at a time.  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 Mar 1, 2019, at 10:57 PM, temban billyhp <btemban at yahoo.com> wrote:
> Hi, 
> How should I vary docking parameters when carrying out ligand/receptor docking in order to obtain correct results. Is there any logical trend to follow. I have always used the default mode. 
> Best regards

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