Re: AMBER: stripping trajectories: ptraj versus Carnal

From: Andy Purkiss <>
Date: Thu, 12 Jan 2006 14:52:14 +0000

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
> 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;
Cat, n.: Lapwarmer with built-in buzzer.
|  Andy Purkiss, School of Crystallography, Birkbeck College, London  |
|           E-mail                   |
|      Phone 020 7631 6869 (Work) or 0776 490 360 (Mobile)            |
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Jan 13 2006 - 06:10:05 PST
Custom Search