AMBER Archive (2006)

Subject: Re: AMBER: stripping trajectories: ptraj versus Carnal

From: Vlad Cojocaru (
Date: Thu Jan 12 2006 - 09:42:41 CST

using the nobox option as described in my previous email creates a file
without box info. However vmd does not read this file neither as crd nor
as crdbox. The topology file that I use is one of the protein without
waters and ions ... (the correctness of the top file is also proved by
the fact that the trajectory output by Carnal is read properly by vmd --
as crd -- with the same top file)...
My impression from analysing the mdcrd output from ptraj is that ptraj
is not outputing only the protein after stripping... Unfortunately, the
trajectory is not read by vmd neither with the topology of the protein
nor with the topology of the protein+water+ions (neither crd nor crdbox)
so I cannot guess exactly what is actually output by ptraj ...

It si interesting that Carlos cannot reproduce this problem... Carlos,
what sintax of the strip command did you use for your case(s)?


Carlos Simmerling wrote:

> this doesn't happen to me- when I use nobox I do not get a box
> and vmd reads it as crd format. This works even when stripping water.
> Of course you can easily check by visually inspecting the trajout output
> using a text editor.
> Andy Purkiss wrote:
>> Dear Vlad,

>> I can't help with the first problem, but for the second one, you think
>> that you have to load the crd file into VMD with the crdbox option. When
>> I run ptraj with strip and then use 'trajout file nobox', I still appear
>> to get the box coordinates written between each frame in the crd file.
>> Andy
>> On Thu, 2006-01-12 at 15:19 +0100, Vlad Cojocaru wrote:
>>> 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
>>> vlad
>>> ptraj input:
>>> trajin ${fname}.mdcrd
>>> strip :462-4993
>>> atomicfluct out fluct-byres.dat @~H* byres
>>> trajout test.mdcrd nobox
>>> go
>>> carnal input:
>>> PARM p ${fname}.top;
>>> STREAM s ${fname}.mdcrd;
>>> COORD c test.mdcrd;
>>> GROUP g (RES 1-461);
>>> COORD c s GROUP g;
>>> END
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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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