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

From: Nitin Sharma <>
Date: Sat, 28 Dec 2013 01:29:06 +0800

Thanks for the reply but I am still confused.

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

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 ? if not then in what scenario one would like to use RMSD without nofit option?

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?

I did try the " 'rmsd' with the 'perres' keyword to calculate per-residue RMSD" and it generated two files one by perresout and another by perresavg option. When I analyzed the perresout file I realized that it contains nofit RMSD values for each residue for every frame. 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 ? Also can you explain what is time-averaged results? If I want to find out residue mobility which column I should choose RMSD_00000[A or RMSD_00000[S.

Thanks and regards,
Nitin Sharma
Department of Pharmacy,Faculty of Science,National University of Singapore,block S7, Level 2, Singapore : ;

-----Original Message-----
From: Daniel Roe []
Sent: Friday, December 27, 2013 10:01 PM
To: AMBER Mailing List
Subject: Re: [AMBER] RMSD vs RMSF vs nofit-RMSD


On Thu, Dec 26, 2013 at 10:40 AM, Nitin Sharma <>wrote:

> I know the definition of RMSD, RMSF and nofit-RMSD i.e. RMSD
> calculates the RMSD by fitting over the reference structure provided
> by the user. RMSF calculates RMSD but with respect to the average
> structure and nofit-RMSD calculates RMSD without fitting against the
> provided reference. Therefore the they give different results.

RMSF is a fundamentally different calculation than RMSD. RMSF (the 'atomicfluct' command in cpptraj/ptraj) is a local measure of motion; it measures the mean fluctuation of atoms, i.e. how much each individual atom moves around (the 'byres' keyword simply averages the results for each atom on a per-residue basis). It is recommended that you RMS-fit to an averaged structure prior to using the 'atomicfluct' command in order to remove global rotational/translational motion, but the fitting is not part of the RMSF calculation itself.

What I should use when I want to see the influence of the mobility of
> particular residues on ligand binding interaction?

For this I think that you can use either '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), or 'atomicfluct' with the 'byres' keyword.

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 Fri Dec 27 2013 - 09:30:03 PST
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