<div dir="ltr"><div dir="ltr">Sure thing, here is what I found in the reply log: <div><br></div><div><div>Autodock Vina ligand docking initiated for 4Q2U.pdb</div><div>Opal service URL: <a href="http://nbcr-222.ucsd.edu/opal2/services/vina_1.1.2">http://nbcr-222.ucsd.edu/opal2/services/vina_1.1.2</a></div><div>Opal job URL: <a href="http://nbcr-222.ucsd.edu/opal-jobs/appvina_1.1.21550104273457-329691785">http://nbcr-222.ucsd.edu/opal-jobs/appvina_1.1.21550104273457-329691785</a></div><div>standard output</div><div>-----</div><div>Inputs arguments: --receptor receptor.pdbqt --ligand ligand.pdbqt --config vina.conf --out results.pdbqt</div><div>Your job 549453 ("vina.sub") has been submitted</div><div>Job 549453 exited with exit code 1.</div><div>-----</div><div>standard error</div><div>-----</div><div>[no output]</div><div>-----</div><div>Traceback (most recent call last):</div><div> 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</div><div> task.statusCBList[0]()</div><div> 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</div><div> self.finishCB(self.backend, fileMap)</div><div> 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</div><div> raise NonChimeraError("No data file returned from "</div><div>NonChimeraError: No data file returned from AutoDock Vina web service</div></div><div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Feb 13, 2019 at 5:55 PM Conrad Huang <<a href="mailto:conrad@cgl.ucsf.edu">conrad@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">That's very odd. The Chimera tool is supposed to detect and download <br>
the data. If it doesn't take too long, can you please try running it <br>
again? When the request is sent, there should be a "status" URL <br>
displayed in the Reply Log. You can use a browser to visit that URL to <br>
check on the calculation. If you can send one of those URLs to me, I <br>
can try to do a little more investigation as to why Chimera is not <br>
behaving properly. Thanks.<br>
<br>
Conrad<br>
<br>
On 2/13/2019 11:53 AM, Cassidy Terrell wrote:<br>
> Hello,<br>
> <br>
> I am using the AutoDock feature in UCSF Chimera and after clicking <br>
> "Apply" everything appears to work normally and then program says: <br>
> E/xecution complete - check outputs to verify successful execution/<br>
> <br>
> In the past a ViewDock window with the results would automatically <br>
> pop-up after the execution completed - however this is no longer <br>
> happening and I do not know how to access the output files. The program <br>
> did not write a /name.pdbqt /file - all other files are there though.<br>
> <br>
> Any suggestions for accessing the output file would be much appreciated!!<br>
> <br>
> -- <br>
> Cassidy R. Terrell, Ph.D.<br>
> <br>
> Assistant Professor, Biochemistry<br>
> University of Minnesota, Rochester<br>
> 111 South Broadway<br>
> Rochester, MN 55904<br>
> <br>
> /Always believe something wonderful is about to happen/<br>
> <br>
> <br>
> _______________________________________________<br>
> Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank">Chimera-users@cgl.ucsf.edu</a><br>
> Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" rel="noreferrer" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br>
> <br>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><font face="tahoma, sans-serif">Cassidy R. Terrell, Ph.D.</font><div><font face="tahoma, sans-serif"><br></font></div><div><font face="tahoma, sans-serif">Assistant Professor, Biochemistry</font></div><div><font face="tahoma, sans-serif">University of Minnesota, Rochester</font></div><div><font face="tahoma, sans-serif">111 South Broadway</font></div><div><font face="tahoma, sans-serif">Rochester, MN 55904 </font></div><div><br></div><div><font face="tahoma, sans-serif"><i>Always believe something wonderful is about to happen</i></font></div><div><font face="tahoma, sans-serif"><br></font></div></div></div>