Dear GMX Community,
I am aiming to compare the relative binding energy (BE) of a ligand to wild
type (WT) vs mutant (MUT) protein and thus trying to run a Free Energy
Calculation for the binding energy of the ligand to both proteins (WT and MUT)
using Bennett Acceptance Ratio (BAR).
As the first step, I calculated decoupling of the ligand from both proteins in
two seperate MD runs by first turning off the coulombic interaction and then
the van der waals interaction. The next step would be the solvation free
energies of the ligand in order to get the correct BE. However, the ligand is
the same for both WT and MUT, so in terms of getting relative BE, should we
still calculate the ligand in water or will the ligand solv energies will
cancel in the DDG=DG(WT)-DG(MUT)?
Besides, from the decoupling of the Protein-ligand complex, I am getting very
high DG values (1134 kJ/mol). Is this meaningful or not?
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