[gmx-users] how to calculate protein-ligand interaction energy?

Mark Abraham mark.j.abraham at gmail.com
Wed Feb 21 12:12:19 CET 2018


You should probably follow the working a paper or tutorial that computes
such a thing. But it probably won't give you a meaningful result, because I
am not aware of a force field that is parameterized so that such a is
meaningful. Computing free energy of binding would be meaningful.


On Wed, Feb 21, 2018 at 12:00 PM Sepide Mofidifar <s.mofidifar at gmail.com>

> Dear Gromacs Users,
> I want to calculate protein-ligand interaction energy. as far as I figured
> out Its summation of these six options in gmx-energy:
> LJ-14: Ligand-Ligand
> Coul-14: Ligand-Ligand
> Coul-SR: Ligand-rest
> LJ-SR: Ligand-rest
> Coul-LR: Ligand-rest
> LJ-LR: Ligand-rest
> I doubt about My calculation. Therefore, it would be helpful if you please
> explain in a bit more detail about calculation of interaction energy, If my
> calculation method is wrong?
> Thanks
> Sepideh Mofidifar
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