Hello all,
I would like just to discuss my idea how to prevent from use of restraints
during decoupling of the ligand
from the receptor (in solvent environment) as a part of absolute free
energy binding calculation using Thermodynamic Integration.
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 (and for each "i" plays the role of "natural" restraint).
If for each "i" the L-Gi interaction is sufficient to prevent ligand from
some unwanted movements, the final dG should be in my opinion
similar to that obtained by decoupling of the whole ligand (all it's
atoms) simultaneously using sufficient restraint.
I wonder if this idea is OK or if is wrong.
Thanks in advance for any comment !
Best wishes,
Marek
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 02 2012 - 17:30:03 PST
