[AMBER] PCA/ essential dynamics

From: Andre C. Stiel <andre.stiel.tuebingen.mpg.de>
Date: Tue, 07 Jan 2014 15:53:55 +0100

there are a number of questions on essential dynamics analysis and its
visualization in the mailing list, but I do not get really consistent
information from it. Most of it seems to be a little outdated. I guess
there are people using this technique maybe they can guide me to some
Here is what I gathered from the archive:

Interactive-ED (IED) ( http://mccammon.ucsd.edu/ied/) - from 2004
running on VMD. I didnt find newer versions or information. And it does
have some issues with the ptraj format as far as I understand.

Pocubine plots: VMD plugin, pymol (using modevectors), BILD

Are there other tools techniques? How do you visualize these movements,
how compatible are the afore mentioned with the cpptraj formats for
modes and projections?

Maybe a little broad question but there is really not to much out there
on PCA - amber - visualization



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Received on Tue Jan 07 2014 - 07:00:02 PST
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