AMBER Archive (2009)

Subject: Re: [AMBER] Protein motions comparison

From: Hannes Loeffler (
Date: Thu Feb 19 2009 - 06:07:47 CST

On Thu, 2009-02-19 at 14:58 +0300, Dmitry Osolodkin wrote:
> 2. Is it correct to compare eigenvalues or eigenvectors between
> different simulations? The proteins differ only by two or three amino
> acid residue substitutions per subunit (ca. 400 residues).

Sure you can but naturally you would have to compare only those residues
that are the same. You have to make sure that your statistics is
sufficient. 6 ns seems to be quite short.

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