I don't have an answer for you since I have never done mmgbsa. But you
might want to check Pin-Chih Su et al's paper (below). They compared all GB
models in Amber.
Su, P.-C.; Tsai, C.-C.; Mehboob, S.; Hevener, K. E.; Johnson, M. E.,
Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA,
MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP
reductase (FabI). Journal of Computational Chemistry 2015, 36 (25),
1859-1873.
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24011/abstract
Hai
On Fri, Oct 23, 2015 at 10:02 AM, anu chandra <anu80125.gmail.com> wrote:
> Dear Amber users,
>
> I am working with a protein-ligand system, where the protein comprise of
> two domains, say A and B and the ligand bind to domain A. I am trying to
> calculate the free energy of ligand binding in presence and absence of
> domain B ( I have carried two different simulations, with and without
> domain B).
>
> With igb=2, I got binding free energy of 85.6 without domain B and
> 91.7 with domain B, and difference is ~6 kcal/mol. With igb=5, the binding
> free energy is 110.5 without domain B and 121.6 with domain B, and
> difference is ~11 kcal/mol. Which values are more reliable, with igb=2 or
> with igb=5? Will it be possible to consider the difference of 6 or 11 (
> either of it depends to the chosen igb value) as a measurement of influence
> of domain B on ligand binding?
>
>
> Many thanks
> Anu
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Received on Fri Oct 23 2015 - 08:30:05 PDT
