Re: [AMBER] problem with the mask syntax

From: Jason Swails <>
Date: Mon, 16 Mar 2015 15:18:13 -0400

On Mon, Mar 16, 2015 at 3:12 PM, George Tzotzos <> wrote:

> Thank you Jason and Kenneth
> I used Kenneth’s script to get topologies stripped of waters and ligands
> (Case 2). parminfo shows the prmtop files to be as expected. When I run
>, it throws the following error
> CalcError: /Users/3i521409/Programs/amber12/bin/cpptraj failed with prmtop
> subA.prmtop!
> Error occured on rank 9.
> Exiting. All files have been retained.
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 9
> Is there a way to troubleshoot this?

cpptraj is dying. Presumably because there is a mismatch in the number of
atoms in the prmtop and the generated coordinate files. Did you remember
to set strip_mask in your input file to get rid of your ligands
as well as solvent? That's the most likely culprit based on what I know of
your workflow.

I would also suggest using in serial on 1 or 2 frames, and then
scaling up once you get that to work.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Mar 16 2015 - 12:30:03 PDT
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