AMBER Archive (2006)

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

From: Andy Purkiss (a.purkiss_at_mail.cryst.bbk.ac.uk)
Date: Thu Jan 12 2006 - 09:01:09 CST

Actually, checking my input, i notice that I had a mistake. I'll check
the correct one and see if I get a box or not!

On Thu, 2006-01-12 at 14:52 +0000, 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:
> >
> > FILES_IN
> > PARM p ${fname}.top;
> > STREAM s ${fname}.mdcrd;
> > FILES_OUT
> > COORD c test.mdcrd;
> > DECLARE
> > GROUP g (RES 1-461);
> > OUTPUT
> > COORD c s GROUP g;
> > END
> >
> >
> >
> > 

-- 
Cat, n.: Lapwarmer with built-in buzzer.
+---------------------------------------------------------------------+
|  Andy Purkiss, School of Crystallography, Birkbeck College, London  |
|           E-mail   a.purkiss_at_mail.cryst.bbk.ac.uk                   |
|      Phone 020 7631 6869 (Work) or 0776 490 360 (Mobile)            |
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