Re: AMBER: Problem with running Sander

From: David A. Case <>
Date: Sat, 7 Jul 2007 21:59:05 -0700

On Sat, Jul 07, 2007, Lili Peng wrote:
> I'm trying to do a classical MD simulation for a pdb file using Sander. I
> have generated the .inpcrd and .prmtop files but when I try to run the
> initial energy minimization, I get this error:
> "*Need to obtain the job magic number in GMPI_MAGIC ! Broken pipe*"

This is not an Amber error message: it comes from your MPI implementation.
It has nothing to do with how you built your topology files, and so on.

Can you run the parallel test cases? If not, that is the place to start,
and you may have to consult your MPI documentation (what MPI are you using?)
If you can run the parallel test cases, look carefully to see if there is
anything different in the way you are running those, and the way you are
running this job (the one that fails).

Others on the list may recognize the exact error message, and be able to
suggest a specific fix....


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Received on Sun Jul 08 2007 - 06:07:56 PDT
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