We need more information.
What version of Amber/AmberTools are you using? Which MM/PBSA script are
you using? What is your input file? What is your *exact* error (not just
part of your error). Based on the provided information it's impossible to
debug any further.
All the best,
Jason
On Mon, May 7, 2012 at 2:58 AM, Jyotsna Bhat <bhat.jyotsna.yahoo.com> wrote:
> Dear AMBER users,
> I am trying to run MMPBSA script on 10 ns simulation trajectory.( My
> protein-ligand complex system has 579 residues. It is a multidomain
> protein; active domain and regulatory domain are situated far away from
> each other, but linked by a large loop. Ligand is present in an active
> domain). Extraction of coordinates is done successfully but during binding
> energy calculation job gets aborted at first coordinate only with the error
> "complex_vac.prmtop not successful".I have tried the adjustment with
> fillratio (2,3 or 4) but it didn't help. Waiting for suggestions
> Thank you.Jyotsna
>
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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 Mon May 07 2012 - 07:30:02 PDT
