AMBER Archive (2006)

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

From: Carlos Simmerling (
Date: Thu Jan 12 2006 - 09:04:45 CST

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.
>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
>>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;

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