AMBER Archive (2006)

Subject: Re: AMBER: modeling of ligand concentrations

From: Sean Rathlef (sean_at_syncitium.net)
Date: Tue Oct 24 2006 - 18:47:03 CDT

On Tue, Oct 17, 2006, Dave Case wrote:

> Once you estimate the
> equilibrium constant from Amber, then (as a separate calculation,
presumably
> just using a slide-rule) you could plug in the actual concentrations of
ligand
> and receptor and compute (for example) the fraction of bound species, etc.
>
> Put another way, the mm-pbsa will give you delta-G-zero (the free energy
> change of the rection at the standard state concentrations). From there,
you
> can compute the free energy change at any other concentrations of your
> choosing (again, in a calculation that is outside of Amber).
>

Just to clarify, say we model the reaction E + A --> EA as single molecular
species in the standard state (everything is at 1M concentration).

2. We obtain a dG^0 of -7kcal/mol from 1M standard state terms.

So, as David says in the above exerpt, if we wanted to compute the free
energy change for any other concentrations, how would we do this? Would
sombody be willing to provide a simple (hypothetical) example? Say our
ligand is 0.1M and our receptor is 0.01M ...

Sean

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