AMBER Archive (2008)

Subject: AMBER: ptraj imaging issue

From: Vlad Cojocaru (
Date: Wed Jun 04 2008 - 14:07:44 CDT

Dear Ambers,

I have noticed a problem with the image command in ptraj9.9e and ptraj9.9h .

When applying the script below with ptraj9.9h (the "e" subversion
behaves the same), I got strangely looking box with one layer of water
separated from the cubic box. Furthermore, I got an warning in the ptraj
logfile connected to the image command ("warning: empty token?"). Now
when I tested the same script with the ptraj from AMBER 9, everything
worked perfectly and no warning appeared in the logfile (everything was
absolutely identical). The trj.dcd is a NAMD generated trajectory with
box info
I couldnt test yet the ptraj from AMBER10 (or AmberTools 1.0).

Is this something that has been observed by others as well ? If its a
known problem, is it fixed in the latest released ptraj from AmberTools
1.0. Or maybe something has changed in the syntax of the image command
(although the manual doesn't indicate that)?


trajin trj.dcd
center ":1-467" origin
image origin center "*"

Dr. Vlad Cojocaru

EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg

Tel: ++49-6221-533266 Fax: ++49-6221-533298


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