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*
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@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@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*
participants (2)
-
Cassidy Terrell -
Conrad Huang