On Tue, Jan 26, 2021, Renato Araujo wrote:
>
>Being able to generate the files, but now you are giving this error. Any
>idea what it might be?
>
>
>Loading and checking parameter files for compatibility...
>sander found! Using /usr/local/chem/amber18/bin/sander
>cpptraj found! Using /usr/local/chem/amber18/bin/cpptraj
>Preparing trajectories for simulation...
>5000 frames were processed by cpptraj for use in calculation.
>
>Running calculations on normal system...
>
>Beginning GB calculations with /usr/local/chem/amber18/bin/sander
> calculating complex contribution...
> File "/usr/local/chem/amber18/bin/MMPBSA.py.MPI", line 100, in <module>
>--------------------------------------------------------------------------
>MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
>with errorcode 1.
Run a short simlation, with just a few frames, using the serial version
of MMPBSA.py. You may get better error messages.
>CalcError: /usr/local/chem/amber18/bin/sander failed with prmtop
>complex.prmtop!
Have you looked at the mdout file from the sander run? Can you run a 1-step
simulation by hand using sander with your complex.prmtop?
Usual debugging advice: if running 5000 frames in parallel fails, try
running a single frame in serial mode. Slowly build up to more complex
situations.
...good luck....dac
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Received on Tue Jan 26 2021 - 11:30:02 PST
