[Chimera-users] Issue with docking in chimera and autodock vina

Elaine Meng meng at cgl.ucsf.edu
Tue May 2 15:46:11 PDT 2017


Dear Alexis,
The AutoDock Vina web service is running (I tried it just now from within Chimera), so I can only say to make sure that the location you’ve specified for any output files on your computer is somewhere reachable and you have permission to read/write files, and that you can overwrite pre-existing files.  Presumably these ligand structures are already open in Chimera, so the only “permission” type problem I could think of was on output.  Normally it will overwrite if you specify the same output name twice, but maybe the directory or file permissions on your system were changed independent of Chimera.
I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On May 2, 2017, at 2:55 PM, Miss Charles <alexis.charles.biology at gmail.com> wrote:
> 
> Dear Chimera Team, 
> 
> I have been trying to dock the small molecules pino-stilbene and trans-stilbene to chainA of the estrogen receptor on chimera using autdick vina. Suddenly, with almost no changes to my protocols I have been getting error message 13 permission of pino-stilbene denied or error message 134 permission of trans-stilbene denied. What am I supposed to do to avoid getting that error message?
> 
> Thank you so much for your time and your help. 
> 
> Sincerely, 
> Alexis Charles 




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