AMBER Archive (2007)

Subject: AMBER: rmsd residue wise

From: ravishk kumar (kumar.ravishk_at_gmail.com)
Date: Thu Jul 26 2007 - 08:02:20 CDT

Dear amber users,
I am trying to plot the residue wise RMSD for a protein.
i tried using this statement in ff.in in ptraj:

 rms out final_eq_rms.out :1-220_at_CA.

But it calculates rmsd time wise with x-axis time frame and y-axis RMSD (of
whole molecule).

how i can i get residue wise RMS with x-axis residue number and y-axis RMSD
(of each residue over all time frame).

I read that CARNAL module can do that. but carnal is not available in
Amber8.

how can i do that?

ravishk

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