afsaneh maleki wrote:
Hi,dear justin,
thanks for your reply
The local destabilization is the subtraction of the thickness of the
bilayer in the membrane protein with thickness of bilayer in the pure
bilayer.
Well, you can certainly get that from the GridMAT-MD output. That's one of the
reasons we designed it. See the previous post for specifics.
-Justin
On Tue, Mar 9, 2010 at 5:53 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
afsaneh maleki wrote:
Hi,
How do i calculate local destabilization of bilayer?
Define "local destabilization."
I can calculate the thickness of the bilayer in the membrane
protein with GridMAT-MD but i can't compare it with thickness of
pure bilayer. Would you please elaborate it clearly?
The output of GridMAT-MD is a projection of thicknesses across the
membrane in the x-y dimensions. You could certainly extract some
useful data (i.e., a radial plot of thickness) out of the output
file using scripting if you wanted. You can use g_dist to get an
"average" thickness, i.e. by using a reference atom in the "top" and
"bottom" leaflets of the bilayer (usually phosphorus). The same type
of radial measurements could be generated with creative use of index
groups, trjorder, and g_dist.
when i calculated thickness of bilayer in membrane protein with
GridMAT-MD i do following as:
./GridMAT-MD.pl param_example
perl convert_to_gnuplot.pl <http://convert_to_gnuplot.pl>
<http://convert_to_gnuplot.pl> 20*20_average.dat 20 20
gnuplot
splot ' 20*20_average.dat' matrix using(1+$1):(1+$2):3
set pm3d map
replot
but "20x20_average_pbc.dat" contains a single column of numbers
and 400 raw line. is it correct?
Yes, per the explanation in our user's guide.
-Justin
Thanks very much in advance,
Afsaneh Maleki
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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