[Chimera-users] Question about AutoDock

[Cassidy Terrell]

Sure thing, here is what I found in the reply log:

Autodock Vina ligand docking initiated for 4Q2U.pdb
Opal service URL: http://nbcr-222.ucsd.edu/opal2/services/vina_1.1.2
Opal job URL:
http://nbcr-222.ucsd.edu/opal-jobs/appvina_1.1.21550104273457-329691785
standard output
-----
Inputs arguments: --receptor receptor.pdbqt --ligand ligand.pdbqt --config
vina.conf --out results.pdbqt
Your job 549453 ("vina.sub") has been submitted
Job 549453 exited with exit code 1.
-----
standard error
-----
[no output]
-----
Traceback (most recent call last):
  File
"/private/var/folders/6k/b103gnf53bs5bd6yy5nqh7sw0000gn/T/AppTranslocation/38672013-1507-4E65-BE74-BEEC2969A32E/d/Chimera.app/Contents/Resources/share/chimera/tasks.py",
line 179, in runStatusCB
    task.statusCBList[0]()
  File
"/private/var/folders/6k/b103gnf53bs5bd6yy5nqh7sw0000gn/T/AppTranslocation/38672013-1507-4E65-BE74-BEEC2969A32E/d/Chimera.app/Contents/Resources/share/WebServices/appWebService.py",
line 172, in statusCB
    self.finishCB(self.backend, fileMap)
  File
"/private/var/folders/6k/b103gnf53bs5bd6yy5nqh7sw0000gn/T/AppTranslocation/38672013-1507-4E65-BE74-BEEC2969A32E/d/Chimera.app/Contents/Resources/share/vina/ws.py",
line 181, in _wsFinish
    raise NonChimeraError("No data file returned from "
NonChimeraError: No data file returned from AutoDock Vina web service


On Wed, Feb 13, 2019 at 5:55 PM Conrad Huang <conrad at cgl.ucsf.edu> wrote:

> That's very odd.  The Chimera tool is supposed to detect and download
> the data.  If it doesn't take too long, can you please try running it
> again?  When the request is sent, there should be a "status" URL
> displayed in the Reply Log.  You can use a browser to visit that URL to
> check on the calculation.  If you can send one of those URLs to me, I
> can try to do a little more investigation as to why Chimera is not
> behaving properly.  Thanks.
>
> Conrad
>
> On 2/13/2019 11:53 AM, Cassidy Terrell wrote:
> > Hello,
> >
> > I am using the AutoDock feature in UCSF Chimera and after clicking
> > "Apply" everything appears to work normally and then program says:
> > E/xecution complete - check outputs to verify successful execution/
> >
> > In the past a ViewDock window with the results would automatically
> > pop-up after the execution completed - however this is no longer
> > happening and I do not know how to access the output files. The program
> > did not write a /name.pdbqt /file - all other files are there though.
> >
> > Any suggestions for accessing the output file would be much appreciated!!
> >
> > --
> > Cassidy R. Terrell, Ph.D.
> >
> > Assistant Professor, Biochemistry
> > University of Minnesota, Rochester
> > 111 South Broadway
> > Rochester, MN 55904
> >
> > /Always believe something wonderful is about to happen/
> >
> >
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription:
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
>


-- 
Cassidy R. Terrell, Ph.D.

Assistant Professor, Biochemistry
University of Minnesota, Rochester
111 South Broadway
Rochester, MN 55904

*Always believe something wonderful is about to happen*
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