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)?
Cheers
vlad
------------------script------------------------------------
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
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
----------------------------------------------------------------------------
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
----------------------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun Jun 08 2008 - 06:07:16 PDT
