AMBER: Problem with running Sander

From: Lili Peng <>
Date: Sat, 7 Jul 2007 16:10:06 -0700

Hi all,

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*"

What does this mean? When I save the topology and coordinate files in
xleap, I get this output:

"Checking unit.
WARNING: the unperturbed charge of the unit: -20.0000 is not a zero.
-- ignoring the warning.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
  total 59 improper torsions applied
Buillding H-bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
     (Residues lacking connect0/connect1 -
        these don't hae chain types marked:

                 res total affected

                 CGLU 1
                 NGLU 1
     (no restaints)

Is it a problem with the building the top and crd files? I can't figure out
why I get a broken pipe. Any feedback and guidance will be greatly

Thanks in advance,

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Received on Sun Jul 08 2007 - 06:07:54 PDT
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