[gmx-users] Simulation of membrane protein

[James Starlight]

Dear Gromacs's users!


I'd like to simulate some membrane proteins in their native environment.

Recently I've found a good tutotial of the same simulation of the KALP
peptide in DPPC membrane (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
).

Is there  someone who have also tried to make thit tutorial ?
First of all its very intresting for me the positioning of the protein in
the membrane via specific  perl script called infrategro. What values for
the cutoff radius as well as measurements of  the area per lipid  are most
adequate for different membrane proteins?

Could you also tell me some alternative ways of full algorithm of the
protein insertion in the membrane?


Thanks,

James
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