Re: [AMBER] Counterion release and Free energy of binding ?

From: Marek Maly <>
Date: Fri, 17 Jul 2009 12:10:40 +0100

Dear prof. Case,

thank you very much for your response.

I read carefully both articles which you suggested and I made this

Calculation of the entropy related to ions organization around the given
polyelectrolyte (cratic entropy)
is already taking in account in relevant Poisson-Boltzman model so it is
probably also implemented in
MM-PBSA Amber routine. If this my conclusion is true, the entropy gain due
to the counterion release during
polyelectrolyte complexation is automatically taking in account in PB part
of the MM-PBSA calculation of the free energy
of binding. Am I right ?

Since frames for the MM-PBSA calculations in Amber contains just "naked"
polyelectrolytes is the effect
of ion atmosphere (entropy, enthalpy) treated some implicit way (like
water) using input parameter ISTRNG
or SALTCON in case of GB model.

Since I am not the expert in this area I would be rally grateful for your
eventual corrections of
my above conclusions.

Thank you very much in advance !

Best wishes


Dne Wed, 15 Jul 2009 05:10:18 +0200 case <>

> On Wed, Jul 15, 2009, Marek Maly wrote:
>> "Entropy and enthalpy of polyelectrolyte complexation: Langevin dynamics
>> simulations"
> You might wish to consult to old-ish, but classic, papers on this
> subject by
> Kim Sharp:
> %A K.A. Sharp
> %A B. Honig
> %T Calculating total electrostatic energies with the nonlinear Poisson-
> Boltzmann equation.
> %J J. Phys. Chem
> %V 94
> %P 7684-7692
> %D 1990
> %A K.A. Sharp
> %T Polyelectrolyte electrostatics: Salt dependence, entropic, and
> enthalpic
> contributions to free energy in the nonlinear Poisson-Boltzmann model
> %J Biopolymers
> %V 36
> %P 227-243
> %D 1995
> Of course, there are lot of other good papers, but these give a nice
> model
> analysis.
> ...dac
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