AMBER Archive (2006)

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

From: Vlad Cojocaru (
Date: Thu Jan 12 2006 - 09:51:57 CST

So, I sent the previous email a bit too early ...

As I suspected, the problem is the sintax of the strip command: if I use
"strip :462-4993" it doesnt work but if I use "strip :WAT" it works but
it strips only the waters and not the ions ... It would be nice if strip
would work with residue numbers ... maybe this qualifies as a bug report
and it would be considered for next release of ptraj ...


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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