Autodock results give a brief breakdown of the free energy contributions by various terms. but the desolvation potential is added up with energy involving hydrogen bonds and van der waal's. is there any method to calculate these parameters separately via AutoDock?
Rogelio Rodríguez-Sotres
You don't.
Autodock does not have that capability, it is intended for the prediction of Protein-ligand of Nucleic acid-ligand interactions.
You can obtain solvation free energy estimates using the FEP methods via MD simulations. The desolvation free energy is the same with a change of sign.
Take a look at this tutorial:
http://www.gromacs.org/@api/deki/files/262/=gromacs-free-energy-tutorial.pdf
Best wishes,
Rogelio
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