On Tue, Jan 03, 2012, Marek Maly wrote:
>
>
> If the ligand L is not too small and several it's atoms are reasonably
> involved into binding interaction with receptor (so it is not the case
> of just one h-bond etc.) the ligand migt be reasonably divided into
> several disjoint atom groups G1,G2 ...Gn and the total decoupling free
> energy dG might be in my opinion calculated as dG = dG(G1) + dG(G2) +
> ... +dG(Gn) where dG(Gi) is the free energy contribution corresponding
> with decoupling of the atom group Gi while the rest of the ligand (L-Gi)
> remains fully interacting....
I don't understand why one would expect your equation to be correct. The
total free energy of decoupling is not just a sum of atomic (or fragment)
energies, at least in general.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 02 2012 - 20:00:03 PST
