VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 12 2010 - 16:46:07 CST

Hi,
  I don't know much about the internal workings of the Maestro plugin
nor the file format itself, so I'm going to defer to the people at
D.E. Shaw Research to try and answer your question, as they developed and
contributed the Maestro plugin for Desmond. I'm CCing Justin Gullingsrud,
hopefully he will have some suggestions for you.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jan 11, 2010 at 10:21:22AM +0100, Jacob Poehlsgaard wrote:
> Hi All
>
> I am trying to make snapshots of a Desmond trajectory as .mae files.
> As I need individual files for each frame I am using a script to loop
> through the frames, writing mae files as I go. The problem now is that
> the files written have 3 entries: protein and ligand, ions and water,
> instead of just having all the atoms in the same entry. I really need
> to have them in the same entry for further processing, so I tried
> setting the same chain for all atoms, but it doesn't change it. Is
> there any way to "collapse" the structure before I write the file?
>
> ---------------------------------------------
> Jacob Pøhlsgaard, Post doc
> Biostructural Research
> Department of Medicinal Chemistry
> PHARMA
> University of Copenhagen
> Universitetsparken 2
> DK- 2100 Copenhagen 

-- 
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