You can use program called HOLE: http://d2o.biop.ox.ac.uk:38080//, it
can calculate the pore profile of your channel.
raja wrote:
Hi all,
I followed center of mass (COM) between lids region (two loops covering
the entrance of active site) during simulation to see its action of
opening and closing. Normally COM varies for all simulation of my
protein (Wild and its mutant variant) is between 17A to 20A. Now I want
to find out the average opening size (Pore or channel size) during
simulation through which the substrate believed to reach the active
site. How to do it either within or outside of gromacs?
With thanks!
B.Nataraj
--
Serge Yefimov
University of Groningen
Department of Applied Physics
Micromechanics of Materials
Nijenborgh 4, 9747 AG Groningen
The Netherlands
tel: +31-50-3634835
fax: +31-50-3634886
e-mail: [EMAIL PROTECTED]
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