Re: [AMBER] Bad atom type error in MMPBSA

From: Jason Swails <jason.swails.gmail.com>
Date: Sat, 24 Dec 2011 09:19:01 -0500

This has been brought up a number of times on the mailing list in the past.
 If you search for "bad atom type mmpbsa", you'll see a number of email
threads that address the issue that I think you're having (but you were
pretty vague about the actual error and didn't provide many details for me
to confirm).

For example: http://archive.ambermd.org/201101/0220.html
http://structbio.vanderbilt.edu/archives/amber-archive/2003/1095.php

Good luck,
Jason

On Sat, Dec 24, 2011 at 7:03 AM, hari krishna <haricoolguy111.gmail.com>wrote:

> Dear all:
>
> I am trying to calculate the binding energy between dna and ligand, with
> that I want to add the K+ ions for the binding energy calculation. I have
> included those ions in the receptor.prmtop with the same sequential
> information in complex.prmtop and all top and crd files.
>
> but while running the gbsa calculation it shows the error bad atom type K
> and MPI is aborted
>
> any suggestions please
>
> regards
> S.Harikrishna
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Dec 24 2011 - 06:30:03 PST
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