AMBER Archive (2009)

Subject: [AMBER] Is it possible to simulate transmembrane protein with GB model ?

From: cgji (
Date: Mon Nov 02 2009 - 14:52:44 CST

Dear Amber users,

    GB parameters used in the software were calibrated according to the water solvents. They may not be suitable for the simulation of membrane environment .
    Any suggestions on changing the parameters are greatly appreciated.
    And only part of the protein was solvated in membrane. Is there a way to solvate the protein into two different implicit solvents (for example water and membrane) ?

   Many thanks for your help in advance.

Best Regards,

Chicago Ji

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