[Chimera-users] Opening DESMOND trajectories in Chimera,

Eric Pettersen pett at cgl.ucsf.edu
Fri Jul 28 11:10:44 PDT 2017

Hi Shriyash,
	Chimera can read Maestro files, but not as a trajectory — I believe you will get a very large number of separate models.
	Using VMD as an intermediary looks like if would work.  You can write a DCD file as per:

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/12717.html <http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/12717.html>

You can also write the corresponding PSF with Extensions  Modeling  Automatic PSF Builder, though you might need to have started from a PDB file — i’m not sure.  There’s a tutorial here:

Generating a Protein Structure File (PSF) <http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node6.html>


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Jul 27, 2017, at 9:46 AM, Shriyash Upadhyay <shriyash.upadhyay at gmail.com> wrote:
> Hello,
> I am a researcher using DESMOND to run molecular dynamics simulations of protein-DNA interactions. However, I and others in my lab are most comfortable viewing trajectories and creating images in UCSF chimera. Is there a way to export DESMOND trajectories in a format that Chimera can open, either from maestro or some intermediate program like VMD?
> Thanks,
> Shriyash Upadhyay
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