Dear Chimera Help Desk, I have a problem while running molecular docking on Chimera. After running Tools --> Surface/Binding Analysis --> AutoDock Vina, I do not get the results from the docking analysis. I get the regular *name*.receptor.pdb , *name*.receptor.pdbqt , *name*.ligand.pdb , *name*.ligand.pdbqt and *name*.conf files, but the *name* file (the docking results) does not generate. In the Reply Log I found this, which I assume is involved in the problem: standard error ----- Unable to initialize environment because of error: cannot register event client. Only 99 event clients are allowed in the system Exiting. ----- Traceback (most recent call last): File "C:\Program Files (x86)\Chimera 1.11.2\share\chimera\tasks.py", line 179, in runStatusCB task.statusCBList[0]() File "C:\Program Files (x86)\Chimera 1.11.2\share\WebServices\appWebService.py", line 171, in statusCB self.finishCB(self.backend, fileMap) File "C:\Program Files (x86)\Chimera 1.11.2\share\vina\ws.py", line 179, in _wsFinish raise NonChimeraError("No data file returned from " NonChimeraError: No data file returned from AutoDock Vina web service And I can't find how to solve this and get the results from the docking experiments I'm doing. Can you please help me solve this problem? Thank you in advance for your attention. Arturo Estolano Cobián <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Libre de virus. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
Hi Arturo, Simon, and Sofia, The message in Arturo’s question below says it is not a Chimera error, but a limit of the Autodock Vina web service, which is run by a different group (as mentioned in the help page, <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>). We do not have direct control over this web service. My guess from reading the message is that there are too many job attempts (>99) causing the error, so I would wait a while and then try again. Trying again immediately or lots of times may make the problem worse. However, this is just a guess, so if you ALWAYS get the same message, maybe there is some other problem. Just now I tried running an Autodock Vina job on the web service and it completed successfully. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 25, 2018, at 8:01 PM, Arturo Estolano Cobián <estolano.arturo@uabc.edu.mx> wrote:
Dear Chimera Help Desk, I have a problem while running molecular docking on Chimera. After running Tools --> Surface/Binding Analysis --> AutoDock Vina, I do not get the results from the docking analysis. I get the regular name.receptor.pdb , name.receptor.pdbqt , name.ligand.pdb , name.ligand.pdbqt and name.conf files, but the name file (the docking results) does not generate.
In the Reply Log I found this, which I assume is involved in the problem:
standard error -----
Unable to initialize environment because of error: cannot register event client. Only 99 event clients are allowed in the system Exiting. ----- Traceback (most recent call last): File "C:\Program Files (x86)\Chimera 1.11.2\share\chimera\tasks.py", line 179, in runStatusCB task.statusCBList[0]() File "C:\Program Files (x86)\Chimera 1.11.2\share\WebServices\appWebService.py", line 171, in statusCB self.finishCB(self.backend, fileMap) File "C:\Program Files (x86)\Chimera 1.11.2\share\vina\ws.py", line 179, in _wsFinish raise NonChimeraError("No data file returned from " NonChimeraError: No data file returned from AutoDock Vina web service
And I can't find how to solve this and get the results from the docking experiments I'm doing. Can you please help me solve this problem? Thank you in advance for your attention. Arturo Estolano Cobián
Hello! Yes, after the error I was trying several times to repeat the experiment, which could have made the problem worse. As you said, today I tried again (after one day) and the docking completed succesfully! Thank you very much for your help. Arturo Estolano Cobián <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Libre de virus. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> 2018-03-26 9:43 GMT-07:00 Elaine Meng <meng@cgl.ucsf.edu>:
Hi Arturo, Simon, and Sofia, The message in Arturo’s question below says it is not a Chimera error, but a limit of the Autodock Vina web service, which is run by a different group (as mentioned in the help page, <http://www.rbvi.ucsf.edu/chimera/docs/ ContributedSoftware/vina/vina.html>).
We do not have direct control over this web service. My guess from reading the message is that there are too many job attempts (>99) causing the error, so I would wait a while and then try again. Trying again immediately or lots of times may make the problem worse. However, this is just a guess, so if you ALWAYS get the same message, maybe there is some other problem.
Just now I tried running an Autodock Vina job on the web service and it completed successfully. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 25, 2018, at 8:01 PM, Arturo Estolano Cobián < estolano.arturo@uabc.edu.mx> wrote:
Dear Chimera Help Desk, I have a problem while running molecular docking on Chimera. After running Tools --> Surface/Binding Analysis --> AutoDock Vina, I do not get the results from the docking analysis. I get the regular name.receptor.pdb , name.receptor.pdbqt , name.ligand.pdb , name.ligand.pdbqt and name.conf files, but the name file (the docking results) does not generate.
In the Reply Log I found this, which I assume is involved in the problem:
standard error -----
Unable to initialize environment because of error: cannot register event client. Only 99 event clients are allowed in the system Exiting. ----- Traceback (most recent call last): File "C:\Program Files (x86)\Chimera 1.11.2\share\chimera\tasks.py", line 179, in runStatusCB task.statusCBList[0]() File "C:\Program Files (x86)\Chimera 1.11.2\share\WebServices\appWebService.py", line 171, in statusCB self.finishCB(self.backend, fileMap) File "C:\Program Files (x86)\Chimera 1.11.2\share\vina\ws.py", line 179, in _wsFinish raise NonChimeraError("No data file returned from " NonChimeraError: No data file returned from AutoDock Vina web service
And I can't find how to solve this and get the results from the docking experiments I'm doing. Can you please help me solve this problem? Thank you in advance for your attention. Arturo Estolano Cobián
participants (2)
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Arturo Estolano Cobián -
Elaine Meng