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
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>
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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