Re: [AMBER] Odd coordinate writing problem in pmemd.MPI SOLVED

From: <>
Date: Wed, 11 Apr 2012 09:20:39 -0400 (EDT)

Hi all,

I figured out the problem, it was not a coordinate writing but a
coordinate reading problem. The weird frames I saw in my crd files were
after it was reduced in size by ptraj, since I couldn't parse the full
10GB file at once. ptraj apparently mangled the coordinates into the
random numbers that puzzled me, so pmemd wasnt doing anything wrong.

The problem is documented and solved in bugfix.9 from AT1.4 (thanks Dan).
Switching to ptraj12 works fine (so would patching my Amber11 installation
on this machine I guess...)

Thanks to all that commented,


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Wed Apr 11 2012 - 06:30:06 PDT
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