Re: [AMBER] Some error in output file and restart

From: Jason Swails <>
Date: Mon, 23 Jun 2014 12:54:08 -0400

On Mon, 2014-06-23 at 11:40 -0400, kirtana S wrote:
> Dear Amber users,
> If I notice asteriosk or stars marks in my output file and restart file
> what does this imply. I had this job run in sander without any issues and
> noticed some error in pmemd cuda. I tried to rectify this by using iwrap 1
> and still notice similar result.

This indicates that the absolute value of some of your numbers are very
large. In restart files this can happen when a particle diffuses
through numerous periodic boxes and goes far away from where it started.
In output files, this typically indicates some type of badly distorted
conformation or incompatibility between the topology and coordinate
files. The former can often be fixed with (careful) minimization. The
latter is user error whose solution depends on what caused the error in
the first place.

In the first scenario (*s in the restart/inpcrd files), wrapping or
using NetCDF restart files should solve your problems. In the latter
(*s in the mdout file), you have to figure out what the real problem is.
Visualizing the structure in VMD should tell you instantly when there is
an incompatibility between the prmtop and inpcrd files. The
"checkoverlaps" command in cpptraj should tell you quickly whether or
not any particles are overlapping, which could lead to the ******s you
see in the mdout file.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Jun 23 2014 - 10:00:03 PDT
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