AMBER Archive (2006)

Subject: Re: AMBER: modeling of ligand concentrations

From: David A. Case (case_at_scripps.edu)
Date: Mon Oct 16 2006 - 19:33:54 CDT

On Mon, Oct 16, 2006, Sean Rathlef wrote:

> > But the *free* energy estimates will know about standard states.
> Basically
> > 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.
>
> Is it possible to adjust the default ligand standard state (1M) to a user
> defined value (or range of values)?

Standard states can be changed, but I doubt that you want to do that. Using
molarity as a concentration is nearly universal in biochemistry: equilibrium
constants are almost always expressed in such units.

I suspect that you are not asking the right question. Maybe you should
explain what you are trying to accomplish. Remember that the standard state
is just a hypothetical reference point: it is only related to the actual
concentrations of species present in any given experiment by giving the units
used. That is the standard state tells you what a concentration of "1" means
(in this case, it means 1 M ).

...hope this helps...dac

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