AMBER Archive (2002)

Subject: Re: combining trajectory file

From: CUI, Guanglei (cuigl_at_morita.chem.sunysb.edu)
Date: Tue Mar 12 2002 - 10:24:44 CST

You may need to remove the title line from the 2nd trajectory on, otherwise,
it wouldn't work correctly.

On Tue, 12 Mar 2002, Natasja Brooijmans wrote:

> You can use ptraj to do this
>
> Best,
>
> Natasja
>
> Natasja Brooijmans
> Graduate Program in Chemistry & Chemical Biology
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> San Francisco, CA 94143-0446
> phone: 415-476 8291
> fax: 415-502 1411
> e-mail: nbrooij_at_itsa.ucsf.edu
>
> On Tue, 12 Mar 2002, Rukman Hertadi wrote:
>
> > HI Amber fans,
> >
> > I am using AMBER 6 recently for my simulation work. I divided my long
> > simulation into several files but I have a problem in combining those files.
> > I tried to use "cat" to cambine them, for example:
> > cat md1.traj > md.traj
> > cat md2.traj >> md.traj
> >
> > However, when I used ptraj to generate the rmsd of the new combined
> > trajectory files, the program did not read the file completely. Anybody who
> > knows to solve this problem, please tell me.
> >
> > Thanks in advance.
> >
> > Rukman Hertadi
> >
> > Laboratory of Biodynamics
> > Graduate School of Biosience and Biotechnology
> > Tokyo Institute of Technology
> >
> >
>
> 

-- 
Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790