[gmx-users] LIE interaction energy calculations

[Bert de Groot]

Anton Feenstra wrote:

> 
> Good idea, but unfortunatly I don't sample the binding/unbinding.
> I have a separate 'unbound' simulation of the ligand in water, and
> several bound simulations of the ligand in the active site. I could
> still get the relative free energies by counting the population of
> the different binding modes, though, but I'm not sure if that helps.
> 


well that would only give you the difference in free energy between
the binding modes, but not relative to the unbound state.

How large is the ligand? Did you consider FEP calculations? (ie
gradually letting the ligand (dis)appear in the pocket -- if you do 
the same in water then the difference between the obtained free 
energies (protein-water) might yield a valuable alternative estimate
of the binding free energy).

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________