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?
I've seen varying reports -- I've seen at least one publication claiming
each is better. They are probably slightly better at slightly different
applications, but I don't remember enough about those publications to give
a definitive answer here. In fact, this difference may not even be
statistically significant (you might be able to compare different GB models
to establish some kind of baseline random uncertainty in this approach, but
I haven't thought too much about that).
I don't even know that there IS a better answer, unless you systematically
evaluate these two models against experimentally *known* results for
similar systems and evaluate for yourself (or see if someone has done such
a study in the literature already).
>
> 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?
That's how I would interpret those numbers.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 23 2015 - 07:30:08 PDT
