Re: amber-developers: Problem in ptraj when using mmpbsa

From: Carlos Simmerling <>
Date: Tue, 14 Mar 2006 16:29:17 -0700

I write out stripped traj files all the time and it works fine.
he must be doing something wrong.

Ray Luo wrote:

> 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.
> Best,
> Ray
Received on Wed Apr 05 2006 - 23:49:40 PDT
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