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
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>
--
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
