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Protein preparation is stalled
https://www.dockingserver.com/forum/viewtopic.php?f=2&t=46
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Author:  ismaelb [ Wed Jan 05, 2011 3:48 pm ]
Post subject:  Protein preparation is stalled

Hello,

I started the preparation of a couple of proteins yesterday. It usually takes few seconds to complete. This time it is in the "waiting" status since about 18 hours. Is something wrong with the server or the pdb file?

Author:  bikadi [ Thu Jan 06, 2011 4:49 pm ]
Post subject:  Re: Protein preparation is stalled

Hello, the jobs are queued based on their priority (subscribers have higher priority), so the job was in queue.

Author:  davecom [ Wed Jun 01, 2011 7:45 am ]
Post subject:  Re: Protein preparation is stalled

bikadi wrote:
Hello, the jobs are queued based on their priority (subscribers have higher priority), so the job was in queue.


I'm having the same issue right now - are there really that many ahead of me at this hour and why aren't they moving along?

Author:  hazaie [ Wed Jun 01, 2011 12:47 pm ]
Post subject:  Re: Protein preparation is stalled

Hi,
I have cheked- all your calculations are done, no calculation is in queue. You have one protein setup which is waiting for user input. If you finish that step you can go ahead and start your docking which is expected to start immediately.
Best regards
Eszter

Author:  vittuperkele [ Thu Jan 26, 2012 2:03 pm ]
Post subject:  Re: Protein preparation is stalled

I still have the problem with the 1o8a - the status is "calculating" but "Calculating protein charges and solvatation parameters (MOPAC2009) – error". What's up with this now?

Author:  bikadi [ Thu Jan 26, 2012 7:12 pm ]
Post subject:  Re: Protein preparation is stalled

This is an error status - PM6 semi-empirical quantum mechanical charge calculation resulted in an error. Unfortunatelly, decoding the exact reason of the error of a quantum mechanical calculation is almost impossible. As you may well know, quantum chemical calculations are very sensitive for any kind of structural problems, missing atoms, bad angles, etc. Please try to analyze your protein structure and if you found problematic regions you should try to fix it. Deleting the N-terminal part and C-terminal part, which is not involved in docking and re-running the calculation on the "core protein" may also help.

Author:  JavenLoh [ Mon Aug 25, 2014 2:37 pm ]
Post subject:  Re: Protein preparation is stalled

bikadi wrote:
Hello, the jobs are queued based on their priority (subscribers have higher priority), so the job was in queue.



Even i have subscribed, the protein setup and docking calculation seems to take ages to be performed.

Author:  bikadi [ Mon Aug 25, 2014 3:46 pm ]
Post subject:  Re: Protein preparation is stalled

When you subscribe, the calculation itself takes more time, because it is carried out with higher accuracy - but you don't have to wait and our processors are working on your dockings.

Author:  JavenLoh [ Mon Aug 25, 2014 3:52 pm ]
Post subject:  Re: Protein preparation is stalled

After i uploaded the protein, status like ' waiting...14/73' will be shown. If i left it unattended, the status sometimes will show waiting for user input. But when i tried to click on it, it directs me to list of error page. Maybe i know why?

Author:  bikadi [ Thu Aug 28, 2014 2:51 pm ]
Post subject:  Re: Protein preparation is stalled

What I see now that you have 40 successful docking calculations in your account. The numbers in queue is for free users, you will jumb to the first position immediately, you are just limited with the number of parallel calculations.

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