VMD-L Mailing List

From: Jacob Poehlsgaard (japo_at_farma.ku.dk)
Date: Wed Jan 13 2010 - 09:15:03 CST

Thanks a lot! The trajectory_in_maeff_out script is not part of our
installation so I wasn't aware of it. I found one called trj2mae in
the latest Desmond download package, and that seems to work perfectly.

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

On Tue, Jan 12, 2010 at 9:52 PM, Miller, Patrick
<Patrick.Miller_at_deshawresearch.com> wrote:
> Another way to do this is to use the "trajectory_in_maeff_out" script that
> comes with Desmond.  This can take any trajectory and create a modified
> .mae file with positions and velocities from an arbitrary frame (it
> defaults to the last frame, but can be set to select by time or by
> frame number).
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Jacob Poehlsgaard
> Sent: Monday, January 11, 2010 4:21 AM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: Maestro file export
>
> 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
>
>