Hi,
On Thu, Dec 26, 2013 at 10:40 AM, Nitin Sharma <sharmanitin.nus.edu.sg>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,
-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 Fri Dec 27 2013 - 06:30:02 PST
