Hi,
On Tue, Feb 26, 2013 at 12:24 AM, Sindrila Dutta banik
<sindrila.duttabanik.yahoo.com> wrote:
> atomicfluct out bfactor-all.dat :1-794 byres bfactor
> Another question, I have 7ns trajectory and I am calculating Bfactor for this trajectory. While the rmsd is less than 5 but the Bfactor is more than 1000 for each residues. Shall I am doing any mistake or there is some problem in my simulation.
The command you give should work. Regarding your question however you
need to make sure you are RMS-fitting your structure to an appropriate
reference (e.g. an averaged structure) prior to the 'atomicfluct'
command (as noted in the manual), otherwise your B-factors will
include contributions from overall rotation/translation movement of
your molecule.
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) 585-9119 (Fax)
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Received on Tue Feb 26 2013 - 14:00:03 PST
