Re: AMBER: Keq computations

From: Carlos Simmerling <>
Date: Mon, 7 May 2007 18:43:53 -0400

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, MM-PBSA 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 <> wrote:
> Dear Amberites,
> I have been trying to reproduce a known Keq value using an MMPBSA method
> in implicit water. My reaction is a host-guest (receptor-ligand) complex in
> the form of:
> R + L <---> RL (Hence, the Keq will have units of M-1).
> 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 (beta-cyclodextrin as host and
> 1-butanol as guest), would we need to model the relative energy for
> 1-butanol 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 M-1)? 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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Received on Wed May 09 2007 - 06:07:20 PDT
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