I am using Amber12 to simulate membrane-protein system with a
combination of ff12SB and Lipid11 forcefields. I have modeled the
system using VMD and converted the files into amber's format. Now, I
am searching for a procedure to simulate the system. I have read Amber
Lipid force field tutorial. But I am not quite sure whether the
procedure given in the tutorial is applicable to a membrane-protein
system. Is there any generalized procedure suggested by the Amber
developers? I found 2-3 procedures in the literature for
membrane-protein simulations. I am not sure which one to choose. Any
help is really appreciated.
mani
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Received on Mon Jan 14 2013 - 21:00:07 PST
