AMBER Archive (2007)Subject: Re: AMBER: Keq computations
From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon May 07 2007  17:43:53 CDT
is your G really G or is it H? meaning have you included
the entropy components? Concentration (relative to std state)
is one part of the entropy calculation you need to include.
In general, MMPBSA is not great at absolute free energies
of association, it is better at relative ones (delta delta G) due
to cancellation of neglected entropy terms (among other things).
On 5/7/07, Sean Rathlef <sean_at_syncitium.net> wrote:
>
> Dear Amberites,
>
> I have been trying to reproduce a known Keq value using an MMPBSA method
> in implicit water. My reaction is a hostguest (receptorligand) complex in
> the form of:
>
> R + L <> RL (Hence, the Keq will have units of M1).
>
> I modeled the 'electrostatic energy in the solvated state' via MMPBSA for
> each species, and computed the gelG from these free energy values as
> follows:
>
> delG = G(products)  G(reactants) = G_RL  (G_R + G_L)
>
> I then computed Keq via:
>
> Keq = e^(delG/RT)
>
> The expected Keq was 7.2, and my value was about 68,000. Seeing as this
> is a standard procedure, this value seems way too high. All species were
> modeled at the standard state of 1M.
>
> Seeing as Keq is not unitless in this case, and in considering that the
> bimolecular step is dependent upon the concentration of L (ligand), where
> did I go wrong? Assuming that Keq is a *constant*, if we were to model
> the expected Keq (7.2) for this reaction (betacyclodextrin as host and
> 1butanol as guest), would we need to model the relative energy for
> 1butanol as a concentration dependent variable?
>
> I guess the main question here is, how can I compute Keq and get a
> respectable result (i.e., ~7 M1)? I'm not using Amber for this
> computation, but I would expect that parameterization of partial charges is
> somewhat conserved from package to package.
>
> Any thoughts would be most appreciated,
> Sean
>
>

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