VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue May 29 2007 - 16:20:56 CDT

Hi Alison,
to start with, you may want to look at the RMSD Trajectory Tool plugin
(http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/rmsdtt/),
which lets you align frames and different structures based on certain
selections and calculate the resulting RMSDs. This is usually a good
step prior to other types of analysis as well. You can find it under the
Extensions->Analysis menu of VMD.

Best,
Peter

Alison Grinthal wrote:
>
> I'm new to VMD and am wondering if someone can provide advice on the
> best way to do the following:
>
> I have a trajectory file from a pulling simulation, and I'm trying to
> compare the structural details of the initial, early, and final
> stages. So first I'm wondering how to overlay structures from
> different frames, while specifying which segment to base the alignment
> on. I'd also like to compare the structure of a given trajectory frame
> with the published structure of the same protein crystallized in
> complex with another subunit (which isn't present in the simulated
> structure's psf file; it's a different pdb file).
>
> More specifically, the protein is composed of sequential repeats, and
> I'd like to analyze how the orientation between adjacent repeats
> changes with pulling. To do this, I'd like to look at 2-repeat units
> from different frames, but align them based only on the first repeat,
> so I can see how the orientation of the second repeat changes relative
> to the first.
>
> Thanks very much for any advice.