[Chimera-users] Question about docking in Chimera

Elaine Meng meng at cgl.ucsf.edu
Wed Dec 20 08:55:14 PST 2017


Hi Rebecca,
Results should open automatically in Chimera (docked ligands shown in main window, additional dialog listing the scores).  I don’t know what happened if it says “execution complete” but you didn’t get any results. You might want to doublecheck that your search box is in the right place relative to the receptor, and that you have specified the output file location as somewhere you have permission to write files, but I really don’t know. The Autodock Vina tool connects to a web service that is run by another group, the NBCR:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

Don’t know what you mean by “prep for some other docking studies”… the prepped input files may be present even if the docking part didn’t produce output.  If you are interested in those, check for the file names and locations specified in the Autodock Vina dialog as “Output file,” see:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

See also the Chimera “Dock Prep” tool which is independent of the Autodock prep:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Dec 19, 2017, at 3:53 PM, Ulrich, Rebecca <ulricr14 at highpoint.edu> wrote:
> 
> Hello,
> 
> I am trying to do some docking studies in chimera and I have been following a protocol given to me in a drug discovery class that walks me through the dock prep and autodock vina options in chimera.  I have tried to run some docking and it will tell me "execution complete- check outputs to verify successful execution" but I don't get any popups with any information about the docking.  Is there a way to get the docking values to show?  I have done this assignment before and didn't have issues, but now as I am redoing it to prep for some other docking studies, I can't get it to work.
> 
> Thanks,
> Rebecca




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