AMBER Archive (2006)

Subject: Re: AMBER: modeling of ligand concentrations

From: Sean Rathlef (
Date: Tue Oct 17 2006 - 11:07:18 CDT

----- Original Message -----
From: "David A. Case" <>
> I'll just assume that you and I mean different things by the term
> state." In my use of the term, changing standard states is trivial.
Since I
> don't understand what you are doing, I probably can't be of much help.

In this regard, the term "standard state" refers to the concentration of
binding ligand. Of course I am looking at larger sets of reactions (as in
an enzyme kinetic mechanism according to conventions of Cleland). To make
this clearer, we could look at a bimolecular reaction (E+A --> EA). The Keq
will related to the difference in dG of the two species, and as such,
equilibrium conditions need to be established. Hence, identification of the
standard state for A needs to be evaluated. This is hard to explain in a
chaper, let alone a paragraph.

> But the *free* energy estimates will know about standard states.
> the standard state of the the ligand (by default, 1M) is included in its
> translational entropy (ditto for the receptor and the complex). So, the
> mm-pbsa procedure would naturally account for ligand concentration.

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?


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