AMBER Archive (2009)

Subject: Re: [AMBER] PCA analysis: the first vector is the movement of whole molecule.

From: Hannes Loeffler (hannes.loeffler_at_stfc.ac.uk)
Date: Thu Jul 30 2009 - 05:52:48 CDT

On Thu, 2009-07-30 at 18:37 +0800, Catein Catherine wrote:
> I have did a PCA analysis, the first vector did not involve movement
> of a sub-domain of the protein, but the rotate/movement of the whole
> protein. While the 2nd and forward vector involve the movement of
> sub-domain. Is it normal results to find the whole molecule
> movement as the first PCA vector? Should I neglect the first PCA
> result in this case?

Are you suggesting to ignore a results because it doesn't meet your
expectations? Are you confident that you have simulated long enough?

> I have used rms first * in the ptraj run already. Did I miss any
> important things or the result is just normal?

The point of initial fitting is to remove rotations and translations.
What does the mask "*" refer to?

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