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

From: Wenyu Qian <>
Date: Fri, 28 Aug 2015 08:55:45 -0600

Hi all,

What we are really interested in is the free energy barrier during the
binding process, which means we need to estimate a free energy "profile"
with respect of reaction coordinate. In this case, is it a good idea to use
umbrella sampling method in AMBER?


On Fri, Aug 28, 2015 at 6:11 AM, David A Case <>

> 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.)
> ....dac
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Received on Fri Aug 28 2015 - 08:00:03 PDT
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