Dear Prof. Jason,
Thanks so much for your helpful reply.
It was found in both cases that the total contribution of
electrostatic (Δ*E*PBCAL + Δ*E*ELE) is positive, which is unfavorable.
Sincerely,
Nadaafiva
On Thu, May 19, 2016 at 8:22 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, May 19, 2016 at 5:19 AM, asdda asa <nadaafiva.gmail.com> wrote:
>
> > Dear Amber users,
> > I calculate binding free energies of a series of ligand-protein complexes
> > using MM-PBSA, and the results show that the electrostatic energy
> > components (Δ*E*ELE) were positive for all complexes, while the polar
> > energies of desolvation (Δ*E*PBCAL) were all negative.
> > Please, what can be inferred from the data.
> > Previously I did the MM-PBSA calculation for different ligand-protein
> > complexes, and the electrostatic energy components were all negatives,
> > while the polar energies of desolvation were all positives.
> >
>
> To me it implies that electrostatic interactions between the ligand and
> receptor are favorable. For example, partially negative groups on the
> ligand interact with partially positive groups on the receptor (or vice
> versa), so that when you *remove* those interactions the electrostatic
> energies of the unbound species is larger than the electrostatic energies
> of the bound species (since it is missing the stabilizing interactions
> between the receptor and ligand in the unbound state, obviously).
>
> But those charge/charge interactions don't just disappear when the complex
> breaks apart, they are replaced by interactions with water. So while the
> loss of electrostatic stabilization in the unbound state results in a
> positive electrostatic binding contribution, the charged active site and
> ligand are more easily solvated, so the polar solvation contribution will
> be negative.
>
> This is a common theme -- solvation and electrostatics typically offset
> (for that precise reason).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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Received on Thu May 19 2016 - 15:30:03 PDT
