AMBER Archive (2006)

Subject: AMBER: stripping trajectories: ptraj versus Carnal

From: Vlad Cojocaru (
Date: Thu Jan 12 2006 - 08:19:17 CST

Dear ambers,

   I am trying to switch from CARNAL to ptraj for truncating amber
trajectories ... In the script below I am trying to strip my periodic
trajectory of waters and ions (keep only the first 461 residues) and
save a trajectory containing only the protein coordinates. However, I
noticed two things: (i) in spite of strip, the atomic fluctuations are
also output for the waters (as far as I read the amber manual this
should not happen), and (ii) I couldn't load the saved trajectory into
vmd as crd format using a topology file of the protein alone (parm7)...
  If I do the same (or I think I do the same) with Carnal I get a nice
trajectory that I can see in vmd (see Carnal input below). Now, the
question is: Are these 2 scripts equivalent (of course regardless of the
atomicfluct command which is additional in ptraj)? Should they produce
the same trajectory or am I wrong here? Maybe my understanding and usage
of the strip command in ptraj is wrong ....
  I would appreciate any advice on this... It would be nice if I could
do everything with ptraj since it has so many nice features now but so
far I am not able to strip trajectories!
Thanks in advance
ptraj input:

trajin ${fname}.mdcrd
strip :462-4993
atomicfluct out fluct-byres.dat @~H* byres
trajout test.mdcrd nobox

carnal input:

   PARM p ${fname}.top;
   STREAM s ${fname}.mdcrd;
   COORD c test.mdcrd;
   GROUP g (RES 1-461);
   COORD c s GROUP g;


Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298

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