AMBER Archive (2003)

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

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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
>
>
>
>
>

• Next message: Lishan Yao: "question about antechamber"
• Previous message: Ling Zhang: "How to put the outside atoms back to the truncated octahedron box?"
• In reply to: Ling Zhang: "How to put the outside atoms back to the truncated octahedron box?"
• Next in thread: Ling Zhang: "The image command of ptraj of Amber 6 is not working."
• Reply: Ling Zhang: "The image command of ptraj of Amber 6 is not working."
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]