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

From: Ray Luo <>
Date: Sun, 12 Mar 2006 22:04:54 -0700

After talking to him, the problem seems to be without using the nobox
option ... Thanks a lot!


Thomas E. Cheatham, III wrote:

>>This is what I did. Read traj file using ptraj. Strip out the atoms I
>>want. Write out a new smaller traj file. The new smaller traj file is
>It is not clear what "garbage" means. Did the user specify the keyword
>"nobox" on the trajout line to avoid dumping box information or was box
>information wanted? Was the first frame OK and all others corrupted
>(usually due to presence/absence of expected/unexpected box information)?

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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