Re: [AMBER] PCA analysis for side chain atoms and backbone atoms

From: Hannes Loeffler <>
Date: Wed, 26 Jan 2011 10:27:02 +0000

On Wed, 26 Jan 2011 10:52:42 +0100
Jorgen Simonsen <> wrote:

> Hi
> Just to be quite sure - I think that I remove as much of the rotations
> and translations by first aligning the atoms
> center :1-100 mass origin
> or for backbone .N,CA,C etc? I hope this is correctly understood.

Centering alone will not remove the rotations. What you should do is
to RMS fit every frame with the same selection that you will use for the
PCA analysis.

> For the side chains, sc, versus backbone.
> For sc, I would like to see how much is captured by the first and
> second principal component and how big a "space" is expanded by this
> side chains. Later, I would like to do quasiharmonic analysis and see
> entropy contribution between bb and sc.

You may have to run very long simulations if you want to quantify this
difference. Keep in mind that the entropy is dominated by
low-frequency modes, i.e. the (possibly much) slower backbone motions.
Those motions will also show up in the side chain analysis. I am not
sure how well both would cancel.

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Received on Wed Jan 26 2011 - 02:30:03 PST
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