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