AMBER Archive (2006)

Subject: Re: AMBER: modeling of ligand concentrations

From: David A. Case (case_at_scripps.edu)
Date: Tue Oct 17 2006 - 11:41:24 CDT

On Tue, Oct 17, 2006, Sean Rathlef wrote:
>
> In this regard, the term "standard state" refers to the concentration of
> binding ligand.

OK, we are using the same term with quite different meanings.

> Perhaps a more appropriate question then would be: can an Amber user
> specify the concentration of the ligand that is interacting with a specific
> receptor? This has to be so, since only in such a way can the true energy
> of the ligand-receptor complex be modeled - but can it be implemented?

This really has nothing to do with Amber per se. 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).

...dac

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