[Chimera-users] Help with Autodock Vina

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 27 17:14:01 PDT 2016

Hi Jonathan,
The Autodock Vina tool in Chimera just runs the Autodock prep scripts and then a web service running Autodock Vina.  We aren’t the developers of the prep scripts or the Vina program, nor do we run this web service, so I can’t really say anything very helpful, sorry.

See manpage with information about the options in the Chimera tool and links to the Autodock website, including their prep scripts:

I guess the first thing to figure out is if the ligand made it through the prep script, or if the failure is later, in the docking calculation.  You can tell seeing if a file appears with name ending in “ligand.pdbqt”.   If the ligand did get prepped but docking didn’t find any positions, it might just be that it does not fit in the site, or no good-enough positions were found with the current level of sampling.  I.e. I’m not sure it means you did something wrong.  I can only suggest looking at the Autodock Vina FAQ or asking your question on their mailing list.


Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 26, 2016, at 11:40 PM, Jonathan Y Wang <wang.ying.jonathan at utexas.edu> wrote:

> To whom it may concern,
> Hi, I was trying to dock a ligand into my receptor and all of the other ligands so far have worked and outputted a value, but this one compound never outputs a .pdbqt file. The other files such as the .conf and .pdb files have been created, the bottom of the screen no longer says "execution in progress", and the green box remains. I've looked at the tutorial for AutodockVina online and tried fidgeting around with it, but I seem to be extremely lost. I was wondering if you had any pointers, tips, or anything at all that could help me.
> All the best,
> Jonathan Wang

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