Dear,

I want to calculate which ligands are better to bind to the specific active site in enzyme.

I figured out calculating binding energies protocol gives helpful informations what I want.

However, I don't know how evaluate resulting values generating from binding energies without "In situ ligand minimization".

I met two problems as below;

(1) Although I didn't use any further calculation processes, the values have different results and tendency depended on which implicit solvent model used.

(2) As I knew, higher value of binding energies means better binding affinity, therefore, a ligand which has higher binding energy is better for specific enzyme, is it right?

Thank you in advance