AMBER Archive (2005)

Subject: AMBER: PCA

From: Claire Zerafa (cporteli_at_waldonet.net.mt)
Date: Tue Oct 11 2005 - 08:33:49 CDT

Dear Amber users

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?

Next,

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

Thanks in advance

claire

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu