nitu sharma wrote:
Hi justin
Thanks for tutorial of membrane protein simulation its
very useful for us . But I want to ask two basic question -
1.The lipid bilayer I have downloded from teleman sir website is so
small in comparision with my protein the suitable box vector for my
protein is 13nm 13nm and 5nm w.r.t XYZ but the lipid bilayer
vector is 6.52270 ,6.54870 ,6.03310. So I want to increase the size of
lipid bilayer w.r.t my protein that means it should be same size.
can you suggest me how "genconf "command useful in doing this .
Well, you already know that genconf is necessary, now read about how to use
-nbox.
2. I want to know the net charge present on my protein can u suggest me
how can it become possible .
pdb2gmx or grompp will tell you in their output, or look at the qtot column in
your .top.
-Justin
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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