Well, one immediate thing that I see wrong here is that you are trying to
run MMPBSA.py in parallel, but you are using the serial version of
MMPBSA.py. In binding_energy.pbs you have the command 'mpirun -np 28
MMPBSA...'. However, to run MMPBSA in parallel you will need to use the MPI
version: MMPBSA.MPI. Essentially, it looks like you are trying to run the
same calculation 28 times and they are competing for resources (same file
names, specifically) and that is what is causing all the errors you are
seeing. Change to the MPI version (or try running MMPBSA in serial instead)
and see if this fixes your problem.
-Bill
On Wed, Sep 7, 2011 at 1:45 PM, Maryam Hamzehee <maryam_h_7860.yahoo.com>wrote:
> Hi,
> Thanks for the reply. I have attached the final results file as well as the
> run files. I am running the calculation as the parallel job on a cluster.
> All commands used are for the different steps are in the ~.pbs files (i.e.
> myscript, run and binding_energy) and the input files are in the ~.in files
> (min, heat, density, equil and prod). I am using Amber 11 and AmberTools 1.5
> on a CentOS cluster which is parallelised by mpi. I submit the jobs to the
> queue and once a job is finished next one in the queue starts.
>
> Cheers,Maryam
> --- On Tue, 6/9/11, Bill Miller III <brmilleriii.gmail.com> wrote:
>
> From: Bill Miller III <brmilleriii.gmail.com>
> Subject: Re: [AMBER] problem with MM-PBSA
> To: "AMBER Mailing List" <amber.ambermd.org>
> Received: Tuesday, 6 September, 2011, 4:09 PM
>
> Are there energies in the FINAL_RESULTS_MMPBSA.dat file? Based on the error
> file you attached it appears as if the PB calculation did not work
> correctly, so I would be very surprised to see the PB binding energy in the
> FINAL_RESULTS_MMPBSA.dat file. What types of calculations were you trying?
> Were you running this in serial or parallel? What command did you use and
> what was your input file?
>
> -Bill
>
> On Tue, Sep 6, 2011 at 4:55 AM, Maryam Hamzehee <maryam_h_7860.yahoo.com
> >wrote:
>
> > Dear Amber List,
> >
> > I am running python version of MM-PBSA for my Ligand-receptor complex.
> The
> > FINAL_RESULTS_MMPBSA.dat is produced successfuly. Among the output files
> > there is a file which has been attached to email named
> > "binding_energy.pbs.e112". I was wondering if you could kindly have a
> look
> > to that file and let me know whether there is a problem in calculation
> with
> > it or not. Can I ignore it?
> >
> > Any help would be highly appreciated!
> >
> > Cheers,
> > Maryam
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Wed Sep 07 2011 - 11:00:05 PDT
