Re: [AMBER] mmpbsa amber error while running decomp

From: Jason Swails <>
Date: Mon, 01 Sep 2014 10:51:16 -0400

On Mon, 2014-09-01 at 05:52 +0000, Sucharita Dey wrote:
> Hello All,
> I am getting this error while running gb and decomp using Amber12 SANDER.
> gb ran successfully in separate. But when try to run decomp with the same
> set of top files it is giving this error :
> mmpbsa amber error failed with prmtop!
> But I checked it prepared some files like _MMPBSA_gb_decomp_com.mdin,
> _MMPBSA_dummycomplex.inpcrd, _MMPBSA_complex.mdcrd.0, (the same for ligand
> and receptor)_MMPBSA_normal_traj_cpptraj.out, _MMPBSA_restrt.0,
> _MMPBSA_complex_gb.mdout.0
> I checked the file _MMPBSA_complex_gb.mdout.0 ,it started writing and
> stopped abruptly after "minimizing coord set # 60"
> Here is my
> input file for running GB in serial
> &general
> startframe=1, endframe=12500, interval=50,

Are you running this in parallel? If so, make sure you look at all of
the output files (i.e., not just the mdout files that end with .0).
Also, try a small number of frames. Does it work if you change endframe
to 200, for instance?

What you have reported contains no error message, so it's impossible to
say what happened. Given the information you provided, it's just as
likely to be a problem outside Amber that killed your calculation as it
is to be a problem inside Amber itself...


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Sep 01 2014 - 08:00:04 PDT
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