Re: [AMBER] RMSD calculation per reside wise not rmse/time by ptraj

From: Jason Swails <>
Date: Sun, 27 Jun 2010 10:52:57 -0400


See the command "atomicfluct" in the AmberTools (or amber) manual. You may
have to install AmberTools-1.4 (available for free on and use
the ptraj compiled there. I would suggest doing this regardless of whether
this functionality is available in the version of ptraj included in amber8.

Good luck!

On Sun, Jun 27, 2010 at 9:55 AM, REENU KHATTRI <>wrote:

> hello sir i am a student and doing project in chimeric RNase A by AMBER 8
> .i
> have been calculated RMSD/TIME and plot the graph but sir i would like to
> know how to calculate RMSD per RESIDE WISE to actual knowing to
> fluctualation in my structures.please send me the script.
> thank you.
> Rinu Khattri
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Sun Jun 27 2010 - 08:00:03 PDT
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