VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 25 2005 - 10:42:40 CDT

Hi,
  Indeed it appears that the crdplugin code writes a group of
zero values for the box information, irrespective of the state
of VMD. This is probably just a placeholder that we intended to
update after reorganizing some code, but it got left in. I've just
updated this code to emit the box side lengths. I'd give you an updated
plugin, but I've recently been making plugin interface changes that make
the newest plugin builds incompatible with VMD 1.8.3. If you want, I can
give you a test version of VMD to try out that includes the new plugin.
Let me know if you want to give that a spin.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 25, 2005 at 11:19:55AM -0400, Guanglei Cui wrote:
> Hi,
>
> I'm trying to use VMD to write AMBER trajectory (crdbox). But I found
> the box dimension isn't actually written in the resulted file. The
> dimension is all zeros. Can anyone confirm on that? Here is what I did:
>
> mol1 = molecule.load("parm7", "prmtop", "crdbox", "mdcrd")
> molecule.write(mol1, "crdbox", "output")
>
> BTW, molecule.get_periodic did return non-zero box dimensions. Thank you.
>
> Regards,
>
> --
> Guanglei 

-- 
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