AMBER Archive (2006)

Subject: Re: AMBER: modeling of ligand concentrations

From: Sean Rathlef (sean_at_syncitium.net)
Date: Tue Oct 24 2006 - 21:30:54 CDT

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Tuesday, October 24, 2006 6:56 PM
Subject: Re: AMBER: modeling of ligand concentrations

> On Tue, Oct 24, 2006, Thomas Steinbrecher wrote:
> >
> > >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 ...
> ^^^^^
> The "..." here is important ---------------- ^. As Thomas has shown, if
you
> start with these concentrations and assume that the system comes to
> equilibrium, you can find all the concentrations. But at equilibrium, dG
is
> zero, so that doesn't help you much (I presume?)

Actually, that does help tremendously. Thank you

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