amber-developers: Problem in ptraj when using mmpbsa

From: Ray Luo <>
Date: Sun, 12 Mar 2006 20:57:52 -0700

Hi All,

An end user here had some problem using ptraj. The following is his
email ... not sure this is a limitation or a bug. He's using Amber 8.

This is what I did. Read traj file using ptraj. Strip out the atoms I
don't want. Write out a new smaller traj file. The new smaller traj file
is garbage. Hence, ptraj is not writing out the file correctly. However,
if you ask ptraj to write out individual coordinate files in the restart
format rather than as one large traj file, each of the individual crd
file is OK. This means one must NOT use the snapshot feature in mm_pbsa.


Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail:
Home page:
Received on Wed Apr 05 2006 - 23:49:40 PDT
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