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Cannot use PM6 for protein
https://www.dockingserver.com/forum/viewtopic.php?f=2&t=86
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Author:  PREACT_Douglas [ Tue Aug 14, 2012 4:58 pm ]
Post subject:  Cannot use PM6 for protein

I have a 3-day subscription but it I get the error that a subscription is required when I try to select the PM6 method for my protein.

Author:  hazaie [ Tue Aug 14, 2012 5:20 pm ]
Post subject:  Re: Cannot use PM6 for protein

Thank you for letting us know, the problem is resolved, you will be able to use PM6 now.

Kind Regards,
Eszter

Author:  PREACT_Douglas [ Wed Aug 15, 2012 11:00 am ]
Post subject:  Re: Cannot use PM6 for protein

Thanks Eszter - it has been computing for a long time, is there a way to check that everything is OK, for example a page where the job queue is visible?

Author:  PREACT_Douglas [ Thu Aug 16, 2012 10:23 am ]
Post subject:  Re: Cannot use PM6 for protein

It's now halted with an error - is there a way I can view what the error is?

Author:  hazaie [ Fri Aug 17, 2012 6:50 am ]
Post subject:  Re: Cannot use PM6 for protein

PREACT_Douglas wrote:
It's now halted with an error - is there a way I can view what the error is?


I have checked your account and found out that one calculation went smoothly, the other resulted in an error. I have checked your protein with an error and there are serious errors in the pdb, there are same chains with the same residues in multiple times but with somewhat different coordinates in the pdb file. Most probably it was an NMR structure originally and it is not properly prepared.

Kind Regards,
Eszter

Author:  PREACT_Douglas [ Fri Aug 17, 2012 9:19 am ]
Post subject:  Re: Cannot use PM6 for protein

Thanks Eszter, apologies for the unusual PDB, I think it has entire segments that were designated as alternate (as opposed to merely side chains).

For the run that completed, I have tried to replicate the successful docking of 2FDP using PM6 charges as described in your paper, however the energies for all 100 runs are positive. Can you spot if I've selected an inappropriate parameter or if there is a problem with the input file(s)?

Author:  hazaie [ Sun Aug 19, 2012 9:29 am ]
Post subject:  Re: Cannot use PM6 for protein

Hi, looks like the simulation box is too small. Please click on the "Restart: Select simulation box" link and select a 30x30x30 sized box.

Eszter

Author:  hazaie [ Sun Aug 19, 2012 9:31 am ]
Post subject:  Re: Cannot use PM6 for protein

I forgot to mention - you have to delete your docking result first, because the protein maps cannot be modified anyway.

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