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

From: Daniel Roe <>
Date: Tue, 31 Dec 2013 09:47:46 -0700


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 Tue Dec 31 2013 - 09:00:02 PST
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