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 - 07:30:03 PDT
