dear dan,
thanks a lot. Yes it cleared almost of all of my doubts.
Regards,
Nitin Sharma
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Wednesday, January 01, 2014 12:48 AM
To: AMBER Mailing List
Subject: Re: [AMBER] RMSD vs RMSF vs nofit-RMSD
Hi,
On Fri, Dec 27, 2013 at 10:29 AM, Nitin Sharma <sharmanitin.nus.edu.sg>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 ?
>
Yes.
> 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,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Jan 01 2014 - 03:00:02 PST
