Hello Catherine,
A lot of users have been trying out membrane bound protein systems recently. There are a variety of parameter sets available for the protein, lipids, and water molecules. In particular for lipids, there are several force fields currently available for MD programs.
Our group has been working on development of a lipid parameter set compatible with Amber called Lipid11. This parameter set was released with Amber 12 as a modular framework for further parameterization. It also includes a new charge derivation for many combinations of gycerophospholipid head groups and tail groups.
Our goal with Lipid11 and future versions of the lipid force field is to create a widely applicable and accessible force field for phospholipid bilayers, including membrane-bound protein systems. We will continue posting updates on this mailing list as well as through the Amber community. Of course, any questions or comments are welcome.
Ben Madej
Walker Molecular Dynamics Lab
________________________________________
From: Catein Catherine [askamber23.hotmail.com]
Sent: Thursday, July 19, 2012 6:24 AM
To: amber.ambermd.org
Subject: [AMBER] Any parameters can be used to model a transmembrane protein?
Dear Sir/Madam,
Any parameters can be used to model a transmembrane protein in AMBER?
Should we use special solvent parameters ?
Best regards,
Catherine
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Received on Tue Jul 24 2012 - 08:30:02 PDT
