i have a general question:
I am going to calculate relative binding efficiencies of a ligand to mutants.
since i have a very large complex, i was thinking of taking only the environment of the binding site (about 30 A in diameter around the site), and to do all the calculations for it only.
(while the most outer shell atoms of the this piece will be fixed, to prevent the whole thing from disintegrating.)
my questions are:
1. what negative implications could this methodology have on the calculations? how "powerful" will be the results? (don't forget ,the calculations are only relative - between such "pieces" that were mutated in the binding site)
2. will these negative implications manifest in MM-PBSA calcs?