Re: How to put the outside atoms back to the truncated octahedron box?

From: Natasja Brooijmans <>
Date: Wed 12 Feb 2003 12:00:50 -0800 (PST)

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

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
Received on Wed Feb 12 2003 - 12:00:50 PST
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