Can you post your MMPBSA.py input file?
On Wed, Jun 12, 2013 at 6:38 PM, Jason Slingsby <jason.slingsby.gmail.com>wrote:
> Dear Amber Users,
>
> I am trying to run a decomposition analysis on a protein and keep running
> into the following error:
>
> bad atom type: N3
> CalcError: /amber12/bin/sander failed with prmtop complex.prmtop!
>
> I have successfully run a different system through the decomp which also
> contained N3 atom types. Looking through the .prmtops I see no differences
> in the way that the amino acids containing type N3 were written between the
> two different systems.
>
> Any ideas as to what could be causing this error? The protein that isn't
> working is a channel made of 5 subunits. I noticed that all subunits begin
> with N3 (on SER and THR residues) Could this have something to do with it
> or is it some other issue?
>
> Thanks,
> Jason
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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 Thu Jun 13 2013 - 11:00:02 PDT
