Hi,
On Sat, Jan 4, 2014 at 10:09 AM, Nitin Sharma <sharmanitin.nus.edu.sg>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,
-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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jan 04 2014 - 11:00:02 PST
