On Wed, Jul 13, 2011 at 11:35 PM, manikanthan bhavaraju <
manikanthanbhavaraju.gmail.com> wrote:
> I am trying to calculate GBSA with amber10 using mm_pbsa.pl in parallel.
> I
> have generated required snapshots. When I running the mm_pbsa.pl script
> for
> GBSA it is giving the following error:
>
> File SANDER is not found.
>
> Execution of the script is done through mpiexec -n 1
> $AMBERHOME/src/mm_pbsa/mm_pbsa.pl binding_energy.mmgbsa > binding.log
>
The perl script is not MPI-enabled. You should not use "mpiexec" in front
of it.
>
> I have even added in the input file
> .PROGRAMS
> SANDER $AMBER/exe/sander.MPI
>
Should that be $AMBERHOME? Also, why are you using sander.MPI? Why not
just "sander"? Is there a "sander" executable in your $AMBERHOME/bin (or
$AMBERHOME/exe)?
HTH,
Jason
> Still I am getting same error. Any insights?
>
> mani
> _______________________________________________
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jul 17 2011 - 04:00:03 PDT
