Re: [AMBER] What is the best way to study a dynamics route of a molecule to enter a protein

From: David A Case <>
Date: Fri, 28 Aug 2015 08:11:22 -0400

On Thu, Aug 27, 2015, Mohammad Salem wrote:
> We are using a green fluorescent protein whose chromophore is
> removed. The protein then has a barrel-shaped structure and there is a
> hollow space inside that can accommodate a molecule (chromophore). We
> then have an idea about the pose it should assume in the pocket. We
> want to see whether the molecule would like to get inserted into the
> interior of the barrel if we have the protein and the molecule freely in
> solution.

I'd recommend against umbrella sampling here if you mainly want to know the
free energy difference between the bound and the unbound states. Consider
free energy methods instead (e.g. chapters 22.1 or 31 in the 2015 Amber
Reference Manual.)


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Received on Fri Aug 28 2015 - 05:30:04 PDT
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