[AMBER] PCA Calculations

From: Parker de Waal <Parker.deWaal.vai.org>
Date: Tue, 30 Jun 2015 02:43:43 +0000

Hi Everyone,

I'm fairly new to PCA and was wondering if someone could help by looking over my input provided here: https://gist.github.com/ParkerdeWaal/da243e14268dcd41f0fa

In this PCA, I am trying to identify stable interactions with a phosphoserine :335, found on protein A, and protein B :350-650.
Specifically, I was wondering how one selects the number of vecs for both the analyze matrix and projection commands.

Using this script above, I am generating 25 eigenvectors, but only projecting on the first 3. As someone that is new to MD PCA, does this sound appropriate?

Finally, from the projection output, how does one decide which modes to plot and obtain kcal/mol as seen here: http://ambermd.org/tutorials/advanced/tutorial22/section3.htm

Any feedback would be greatly appreciated!

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Received on Mon Jun 29 2015 - 20:00:03 PDT
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