AMBER Archive (2003)

Subject: Re: structure image

From: A.Madhumalar (malar_at_mbu.iisc.ernet.in)
Date: Mon Jan 27 2003 - 19:51:35 CST

Hi,
   You can use trnsform command in rdparm to get all the coordinates in
the central box,it needs parmtop & mdcrd files.

On Mon, 27 Jan 2003, Xiang, Tian-Xiang wrote:

> Dear Sir:
>
> I am trying to prepare an image of my simulated lipid bilayer structure obtained from
> sander/amber using a graphics program like VMD, but some molecules are always
> stretched out of the central box. This can not be solved by using "image" command in ptraj. The one way I can think of is that somehow one can get the image of the central box along with the neighboring boxes. Anyone has ideas how to do this or a better way?
>
> Thanks
>
>
> T.-X. Xiang
>