Re: [AMBER] standard for atomic fluctioantion

From: Daniel Roe <>
Date: Sat, 4 Jan 2014 11:34:53 -0700


On Sat, Jan 4, 2014 at 10:09 AM, Nitin Sharma <>wrote:

> I am aware of the 2 Angstrom as a benchmark for RMSD but is there any
> benchmark for atomic fluctuation too? How I can say by looking just at
> atomic fluctuation result which residue is moving within acceptable range
> and which is not?

I'm actually wary of calling 2 Angstroms a "benchmark" for RMSD, by which I
assume you mean something like a cut-off for determining a 'native' state.
This number is going to be both system dependent (e.g. 2 Ang. for a 5
residue polypeptide may be too large a cut-off, while 2 Ang. for a 700+
residue peptide may be too small) and selection dependent (i.e. all-atom
versus backbone atoms versus mass-weighted, etc). You will need to look at
the actual behavior of your system to determine what a reasonable cut-off
is. If you're trying to do something like determine a melting curve, your
results could be quite sensitive to how you choose your cut-off.

Similarly, I don't believe there is one value that atomic fluctuations
should be compared to - they will be system dependent as well. For atomic
fluctuations you ideally want to compare to some experimental measure of
atomic mobility such as B-factors from an X-ray crystal structure (for
which you can use the 'bfactor' keyword with the 'atomicfluct' command in
cpptraj / ptraj).

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 Sat Jan 04 2014 - 11:00:02 PST
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