Hello,
I have a trajectory of an explicitly solvated holo-enzyme (with the ligand bound) that I want to calculate the binding energy for. Binding energy is the sum of electrostatic interactions and Lennard Jones potential. I am currently working on Discovery Studio 2016 which requires me to supply the dielectric constant of the system. The ligand interacts with both the amino acid residues and the surrounding water. Since the dielectric constant ε for the enzyme = 4, and for water=80, which one shall i choose ?
I did choose ε = 1 but I did overestimate the electrostatics didnt I ?
Philippe Derreumaux
See recent review:
Tuffery P, Derreumaux P.
J R Soc Interface. 2012 Jan 7;9(66):20-33. doi: 10.1098/rsif.2011.0584.
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