[gmx-users] Hydrophobic interaction energy

Sun Iba sun.iba2 at gmail.com
Wed Sep 7 19:54:34 CEST 2016

How would you define hydrophobic energy? I mean I have heard of hydrophobic
effect that arises due to solvent but this term is new to me. You can
calculate van der Waal term with MM-PBSA etc. People use this energy term
to highlight the role of hydrophobic and non-polar amino acid residues
towards total binding free energy. There are numerous papers in this area.
I don't know how important hydrophobic energy is to you but it seems
difficult to calculate it between protein and ligand particularly. I am not
sure there is a tool.

On Wed, Sep 7, 2016 at 8:22 PM, Nikhil Maroli <scinikhil at gmail.com> wrote:

> For a particular system I wanted to know the hydrophobic energy between the
> ligand and proteins apart from Electro and van der Waals.what is the
> possibility in gromacs? or any other tools available for the same?
> --
> Regards,
> Nikhil Maroli
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