[Chimera-users] Problem with autodock vina in chimera

Elaine Meng meng at cgl.ucsf.edu
Fri Jan 17 16:27:36 PST 2020

Also, it sounds like you might have been looking at the ligand pdbqt file (which is created so that it can be used as input to the docking step), not the docking results pdbqt file.  The different pdbqt files are described in the manual page under “Output file”: 



> On Jan 17, 2020, at 3:19 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi,
> I tried Chimera’s Autodock Vina interface to the web service twice today after you sent this message as a bug report, I do not see this problem: it returned results to me normally.
> When results are available, Viewdock starts automatically and shows the results; you would not need to start it yourself.  I do not get any message about a results directory.  Tested using a recent version of Chimera.  If I show the Reply Log (open from Favorites menu) it says something like this when the calculation finishes:
> Job 669753 exited with exit code 0.
> It may be that even though the calculation finished, because of your specific structures and choices of input parameter values, there are zero results. Or, you did not wait long enough for the calculation to finish and they were not yet written to the pdbqt file even though that file existed.  
> However, importantly, you should be aware that this docking web service only allows very little sampling and is not suitable for most research purposes, as stated in the boxed warning on the manual page:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.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 Jan 16, 2020, at 10:00 AM, De campos, Luana J <luana.decampos at unmc.edu> wrote:
>> Hi,
>> I am using the option autodocking vina in chimera and I have a problem related to the docking results. I set up the docking parameters all correct and initiate the docking run. Apparently, everything goes well, I even receive a message in chimera saying that I can see the results in the directory chosen. However, when I use the option "ViewDock" I can not see the results and I get I message saying that the file .pdbt does not appear to be dock out. Also, the docking calculation goes really fast, not like before that I used to take some time. In my inspection of the .pdbqt file created in the directory from the docking calculation (using note pad) it just has the compounds and the flexible bonds, it does not have the energies of the complexes ligand-protein. 
>> Is there any way to correct this bug?
>> Thank you very much. 
>> Luana de Campos
>> Pharmaceutical sciences PhD. student
>> University of Nebraska Medical Center

More information about the Chimera-users mailing list