It might seem like a strange opinion from a GB model developer, buy I don't
usually recommend GB for binding affinity post-processing. We use GB where
speed is crucial, such as in md. For post-processing you're not doing it
for each time step, so I prefer using a better PB. GB just isn't as good as
PB, and if you have the choice then why use something less accurate? It's
not likely that the speed of the PB calculation will be the limiting favor
in this project. For md, it definitely is so we use GB there. GB also tends
to be not as well trained for chemical diversity.
Others may have different opinions, this is just mine...
Carlos
On Oct 23, 2015 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 - 12:30:03 PDT
