[Chimera-users] question about AutodockVina /CHIMERA

ogs ogs at ibt.unam.mx
Mon Jan 22 12:25:47 PST 2018

 Thank you so much for your answer.

 I tried to repeat docking I did before (when I got output) and I did 
 not see the output this time.
 I only get: receptor.pdbqt and ligand.pdbqt as output. I did not get 
 the name.pdbqt file. The software did not show any warm message or 
 something like that.

 Osvaldo Gómez

 On Fri, 19 Jan 2018 18:31:07 -0800, Elaine Meng <meng at cgl.ucsf.edu> 
> A few more points:
> If there is docking output, it would appear automatically in Chimera.
> That is, you would see docked structure(s) in the 3D graphics window,
> and a ViewDock dialog listing these results and their scores.  I 
> guess
> you didn’t get that either.  Some things to check are that your
> receptor and ligand pdbqt files seem reasonable (do they contain the
> expected atoms?) and that the search box is a reasonable size and
> location.  If the search box is completely filled with receptor 
> atoms,
> there might not be any space to put the ligand, for example.
> These are all just guesses of possible things that could go wrong. I
> don’t know if they apply to you or not.
> Best,
> Elaine
>> On Jan 19, 2018, at 4:28 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> Hi Osvaldo,
>> Without more information, I have no idea, sorry.  If you are sure 
>> that the process finished (click the “i” icon near the bottom right 
>> corner of the Chimera window to make sure), I can only say to check in 
>> the Reply Log (open from Chimera Favorites menu) and see if it says 
>> anything else useful.  The Autodock Vina process does not run on our 
>> system, so there is nothing I can check here; Chimera just has an 
>> interface to send and receive results from a web service that is run 
>> by another lab, as explained in the help page:
>> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
>> For the future, please send Chimera questions to the 
>> chimera-users at cgl.ucsf.edu address (CC’d here) to ensure they come to 
>> our attention.
>> 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 19, 2018, at 4:04 PM, ogs <ogs at ibt.unam.mx> wrote:
>>> to whom it may concern,
>>> hi!
>>> I am having some problems using AUTODOCK-VINA / CHIMERA.
>>> I recently docked a linand, but I did not get the name.pdbqt file 
>>> as result (I only got the name.receptor.pdb and pdbqt and the 
>>> name.ligand.pdb and pdbqt)
>>> The software show a message telling me that the process has ended 
>>> and I need to check the files (but I did not see the name.pdbqt file)
>>> What is happening? What could I do to solve this problem?
>>> Thanks a lot.
>>> Osvaldo Gómez Secundino

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