AMBER Archive (2003)

Subject: The image command of ptraj of Amber 6 is not working.

From: Ling Zhang (lz267_at_nyu.edu)
Date: Wed Feb 12 2003 - 14:36:58 CST

I did try the image command of ptraj in Amber 6. But it is not working. And the transform command of rdparm in Amber 6 is obsolete. So is there any way else that I can put the outside atoms back? Thanks.

Best,
Ling
----- Original Message -----
From: "Natasja Brooijmans" <nbrooij_at_itsa.ucsf.edu>
To: "Ling Zhang" <lz267_at_nyu.edu>
Cc: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Wednesday, February 12, 2003 3:00 PM
Subject: Re: How to put the outside atoms back to the truncated octahedron box?

> Have you tried ptraj? Instructions are in the manual, which can be found
> on line.
>
> 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 Wed, 12 Feb 2003, Ling Zhang wrote:
>
> > Dear All:
> >
> > I used truncated octahedron box for simulation using Amber 6. And some of the atoms drifted out of the period box. The image option of Amber 6 is not working. And Amber 5 can't recognize the truncated octahedron box shape. Is there a way that I can put the outside atoms back in the box? Thanks a lot.
> >
> > Best,
> > Ling Zhang
> >
> >
> >
> >
> >
>