VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 29 2004 - 10:56:26 CDT

Hi,
  If you load the Amber files with the "crdbox" version of the crd
reader plugin, it should correctly load your file. Once loaded,
you should be able to use the controls in the "periodic" tab to
see additional periodic cell images. The main issue is correctly
loading your Parm/CRD files. You didn't specify which version of
Amber you're using, just make sure to use the "parm7" for Amber 7.x
and "parm" for the older versions.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 28, 2004 at 11:25:09AM -0400, Xiang, Tian-Xiang wrote:
> Dear Sir:
>
>
>
> I have an Amber coordinate .crd file with box conditions. How can I
> display the molecules in the center box
>
> along with those in the neighboring image cells. Since my system is a
> polymer, many polymer segments extend
>
> beyond the center box such that the system displayed contains many
> artificial holes. If I can also display the image cells, maybe
>
> the holes can be filled this way. In all, I want to display an image
> fully filled with the molecules without artificial holes.
>
>
>
> Any suggestions are appreciated.
>
>
>
> Xiang
>
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078