Hi Marek and all.
I agree with Dave Case that this is not correct. If the ligands where
just the sum of its 'parts', life would be MUCH easier. Unfortunately,
it is not.
What one 'could' do is to decouple G1, THEN G2 (with G1 decoupled), THEN
G3 (with G1, G3 decoupled), etc, in a sequential way. This must be
exactly the same as decoupling all at the same time. It is in fact a
'path' that connects the same initial and final states. I just cannot
imagine it being more efficient than the usual way.
Adrian
On 1/2/12 10:38 PM, case wrote:
> 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
--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 03 2012 - 07:30:02 PST
