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<p class="MsoNormal">Hi,dear justin,</p><p class="MsoNormal">thanks for your reply</p><p class="MsoNormal"></p><p class="MsoNormal">The local destabilization <span style=""> </span>is the subtraction of the thickness of the bilayer
in the membrane protein with <span style=""> </span>thickness
of bilayer in the pure bilayer. <br></p><p class="MsoNormal"><br></p>
<br><br><br><br><div class="gmail_quote">On Tue, Mar 9, 2010 at 5:53 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
afsaneh maleki wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
How do i calculate local destabilization of bilayer?<br>
</blockquote>
<br></div>
Define "local destabilization."<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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?<br>
<br>
</blockquote>
<br></div>
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.<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
when i calculated thickness of bilayer in membrane protein with GridMAT-MD i do following as:<br>
<br>
./GridMAT-MD.pl param_example<br></div>
perl <a href="http://convert_to_gnuplot.pl" target="_blank">convert_to_gnuplot.pl</a> <<a href="http://convert_to_gnuplot.pl" target="_blank">http://convert_to_gnuplot.pl</a>> 20*20_average.dat 20 20<div class="im">
<br>
gnuplot<br>
splot ' 20*20_average.dat' matrix using(1+$1):(1+$2):3<br>
set pm3d map<br>
replot<br>
<br>
<br>
but "20x20_average_pbc.dat" contains a single column of numbers and 400 raw line. is it correct?<br>
</div></blockquote>
<br>
Yes, per the explanation in our user's guide.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Thanks very much in advance,<br>
Afsaneh Maleki<br>
<br>
</blockquote>
<br></div>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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