Re: [AMBER] RMSD vs RMSF vs nofit-RMSD

From: Nitin Sharma <>
Date: Wed, 1 Jan 2014 18:51:27 +0800

dear dan,

thanks a lot. Yes it cleared almost of all of my doubts.

Nitin Sharma

-----Original Message-----
From: Daniel Roe []
Sent: Wednesday, January 01, 2014 12:48 AM
To: AMBER Mailing List
Subject: Re: [AMBER] RMSD vs RMSF vs nofit-RMSD


On Fri, Dec 27, 2013 at 10:29 AM, Nitin Sharma <>wrote:

> If I understood it correctly the RMSD calculated against the average
> structure WITHOUT using nofit option will give different result as
> compared to atomicfluct after RMS-fit to the average structure

Yes - as I said before, RMSD and RMSF are inherently different metrics.

> As you have recommend me to use " 'rmsd' with the 'perres' keyword to
> calculate per-residue RMSD (which is a global RMS-fit followed by a
> no-fit RMSD calculation for individual residues)" does that mean rmsd
> fit option is just to overlap a certain structure while main result is
> counted for nofit ?


> I can understand the examples when one wants to superimpose a subunit
> A1 with subunit B1 of the reference and calculate the nofit rmsd for
> subunit
> A2 against B2. However, in the my case when reference is complete
> protein for global RMS-fit in first step then how does nofit works in
> second stage ? is this because only backbone is superimposed and not
> the side chains of the residues?

The global fit is to remove as much of the overall difference between the target and reference structures as possible. The 'nofit' for each individual residue then provides a more local measure of RMSD. Two additional things I can recommend when using the 'perres' option: 1) try not including backbone atoms in the 'perres' stage with the 'perresmask'
keyword, e.g. "perresmask &!.H,N,CA,HA,C,O", and 2) try using the 'perrescenter' keyword, which centers each residue prior to the 'nofit'
calculation; this is useful for isolating changes in residue conformation.

The perresavg file contained three columns #Residue, RMSD_00000[A and
> RMSD_00000[S. The RMSD_00000[A as I see contains the average of the
> RMSD values present in perresout file. However, I am not able to
> figure out what RMSD_00000[S column signifies ?

First, you should update your version of cpptraj since a recent patch has fixed the truncation of data set names when they are larger than the column size. The "RMSD_00000[A" column contains the average values (as you surmised), and the "RMSD_00000[S" contains the standard deviations.

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Jan 01 2014 - 03:00:02 PST
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