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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