AMBER: rmsd residue wise

From: ravishk kumar <>
Date: Thu, 26 Jul 2007 18:32:20 +0530

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

 rms out final_eq_rms.out :1-220.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

how can i do that?


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Received on Sun Jul 29 2007 - 06:07:22 PDT
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