Re: [AMBER] PrmtopError: Complex natom != receptor natom + ligand natom

From: David A Case <>
Date: Tue, 26 Jan 2021 14:19:55 -0500

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/", 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 You may get better error messages.

>CalcError: /usr/local/chem/amber18/bin/sander failed with 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

...good luck....dac

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Received on Tue Jan 26 2021 - 11:30:02 PST
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