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 Post subject: Cannot use PM6 for protein
PostPosted: Tue Aug 14, 2012 4:58 pm 

Joined: Thu May 24, 2012 3:11 pm
Posts: 4
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.


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 Post subject: Re: Cannot use PM6 for protein
PostPosted: Tue Aug 14, 2012 5:20 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 40
Thank you for letting us know, the problem is resolved, you will be able to use PM6 now.

Kind Regards,
Eszter


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 Post subject: Re: Cannot use PM6 for protein
PostPosted: Wed Aug 15, 2012 11:00 am 

Joined: Thu May 24, 2012 3:11 pm
Posts: 4
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?


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 Post subject: Re: Cannot use PM6 for protein
PostPosted: Thu Aug 16, 2012 10:23 am 

Joined: Thu May 24, 2012 3:11 pm
Posts: 4
It's now halted with an error - is there a way I can view what the error is?


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 Post subject: Re: Cannot use PM6 for protein
PostPosted: Fri Aug 17, 2012 6:50 am 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 40
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


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 Post subject: Re: Cannot use PM6 for protein
PostPosted: Fri Aug 17, 2012 9:19 am 

Joined: Thu May 24, 2012 3:11 pm
Posts: 4
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)?


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 Post subject: Re: Cannot use PM6 for protein
PostPosted: Sun Aug 19, 2012 9:29 am 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 40
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


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 Post subject: Re: Cannot use PM6 for protein
PostPosted: Sun Aug 19, 2012 9:31 am 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 40
I forgot to mention - you have to delete your docking result first, because the protein maps cannot be modified anyway.


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