AMBER Archive (2009)

Subject: Re: [AMBER] Simulating transmembrane protein.

From: case (
Date: Mon Oct 12 2009 - 16:55:42 CDT

On Mon, Oct 12, 2009, Jayalakshmi Sridhar wrote:
> I would like to do MD simulations on a receptor protein- it has
> extracellular region, transmembrane region and intracellular region. Is it
> possible to carry out MD simulation of the entire protein with parts of the
> protein in different solvent boxes. How can I specify a particular solvent
> box for one part of the protein and a different solvent box for the next
> part of the protein?

As Bill Ross pointed out, you don't really have different "boxes". The
Schulten group has some nice tutorials on simulations of membrane proteins +
membranes + water:

...good luck...dac

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