From: David A. Case <>
Date: Tue, 11 Oct 2005 07:32:36 -0700

On Tue, Oct 11, 2005, Claire Zerafa wrote:
> I am running dynamics runs for the first time on Amber and I have these
> questions
> .mdcrd file is a list of xyz co-orodinates with time is it not? There is no
> measure of atom velocity or torsion or rotational changes is there?

Your description is correct.

> I want to perform pca on the output of my dynamics. Pls can anyone tell me
> what would constitute good reading material about pca on protein

I wouldn't hurt to look at some of the original literature:

%A A. Amadei
%A A.B.M. Linssen
%A H.J.C. Berendsen
%T Essential dynamics of proteins
%J Proteins
%V 17
%P 412-425
%D 1993

%A D.M.F. van\0Aalten
%A B.L. de\0Groot
%A J.B.C. Findlay
%A H.J.C. Berendsen
%A A. Amadei
%T A comparison of techniques for caclulating protein essential dynamics
%J J. Comput. Chem.
%V 18
%P 169-181
%D 1997

Searching for the term "essential dynamics" will also yield lots of other

> and also what software is normally used to handle the large
> data volume produced by dynamics runs

Amber's ptraj program is certainly a good choice.


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Received on Tue Oct 11 2005 - 15:53:01 PDT
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