AMBER Archive (2006)

Subject: Re: AMBER: modeling of ligand concentrations

From: Sean Rathlef (sean_at_syncitium.net)
Date: Mon Oct 16 2006 - 20:37:25 CDT

From: "David A. Case" <case_at_scripps.edu>
> > 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.

If you are saying that indeed the standard states can be changed, then I may
be in a good way. I have been struggling with methods to do this for some
time. We must talk !!

> 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 ).

Our need (form some enzyme kinetics simulations) is to model changes in
standard state concentrations until such time as the equillbrium constant,
modeled from concentrations, is equilvalent to the equilibrium constant
modeled from forward and reverse rate coefficients. Typically, we start
with ligand concentrations at or near the dissociation constant, and adjust
them iteratively. It is a process we are testing called equilibrium
convergence.

I'd like to give away more of the details, but it is a proprietary method.
We are testing this out on some viral enzymes at the University of Victoria
presently. As of this email, I may be interested in looking at Amber along
with the other three suites we are testing. Can it be arraged for us to
gain access to academic Amber 9.0 for some tests at UVic for a couple of
months?

Sincere thanks David - this is very helpful indeed ... I'd be happy to
provide some more details perhaps over the phone, maybe tomorrow (?)

Sean

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