VMD-L Mailing List

From: Jacob Poehlsgaard (japo_at_farma.ku.dk)
Date: Mon Jan 11 2010 - 03:21:22 CST

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?

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Jacob Pøhlsgaard, Post doc
Biostructural Research
Department of Medicinal Chemistry
PHARMA
University of Copenhagen
Universitetsparken 2
DK- 2100 Copenhagen