Sure, I will read that paper. The systems consists of 256 POPC
molecules, 13 cholesterol molecules, and the protein (355 residues + 2
Ca+2 ions). The POPC bilayer has a cylindrical hole (radius = 12 ang)
in the center. Using VMD, I have manually inserted the protein into
the cylindrical hole i.e. 1-20 residues and rest of the protein is
above the bilayer. Then, I have manually added the cholesterol
molecules and then solvated the system. The protein has -10 charge so
I have added 10 Na+ ions. The total size of the system is 100*100*140.
Further, I am maintaining 0.15M KCl concentration (127 K+, 127 Cl-
ions) for the entire system. I am interested to analyze the
interactions between the protein's 1-20 residue with the bilayer. In
my case, the protein is just bound to the membrane not does not cross.
mani
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Received on Tue Jan 15 2013 - 10:30:02 PST
