Dear Amber Users,
I'm now running the simulation of the protein (GPCR) embedded in membrane
using lipid11 and ff99SB force field. I used the parameters as in the
tutorial. The simulation is going good. However, I would like the check the
quality of my membrane protein like the area per lipid, thickness of the
membrane, electron-density profile and some other parameters. Are there
some tutorials how can I calculate all those properties for the membrane
protein and what else parameters do I have to check? or in fact the lipid11
force field is already well validated and tested according to the
J.Phy.Chem B, 2012, so I can use the lipid11 force field for my simulation
without checking the quality again.
Best Regards,
Kanin Wichapong
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Received on Fri Jul 05 2013 - 14:00:03 PDT
