You should check your _MMPBSA_complex_gb.mdout (or
_MMPBSA_complex_gb.mdout.#) output file. It will hopefully have a more
detailed error message since the error actually occurred while attempting
the GB calculation of the complex.
And just to be sure, you said that the prmtop loaded correctly in
VMD/Chimera, but did you try loading the prmtop _and_ the
_MMPBSA_complex.mdcrd (or _MMPBSA_complex.mdcrd.#) created by MMPBSA.py
into VMD?
-Bill
On Tue, Feb 25, 2014 at 11:52 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi everybody,
>
> I checked the archive to see if I could identify the source of error
> occurring "on rank 0". I didn't find anything that really makes sense to
> me. The prmtop file identified in the log (see below) loads correctly in
> VMD and Chimera.
>
> Any help would be much appreciated.
>
> Last but not least all patches have been applied successfully.
>
> Log file output follows below
>
> Thanks in advance
>
> George
>
>
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using
> /Users/3i521409/Programs/amber12/bin/mmpbsa_py_energy
> cpptraj found! Using /Users/3i521409/Programs/amber12/bin/cpptraj
> Preparing trajectories for simulation...
> 1000 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with
> /Users/3i521409/Programs/amber12/bin/mmpbsa_py_energy
> calculating complex contribution...
> CalcError: /Users/3i521409/Programs/amber12/bin/cpptraj failed with prmtop
> 4fqt_OVT.prmtop!
> Error occured on rank 0.
> Exiting. All files have been retained.
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>
>
> ===================================================================================
> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> = PID 52649 RUNNING AT itvds-ws026.local
> = EXIT CODE: 1
> = CLEANING UP REMAINING PROCESSES
> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>
> ===================================================================================
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>
--
Bill Miller III
Post-doc
University of Richmond
417-549-0952
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Received on Tue Feb 25 2014 - 12:30:07 PST
