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

[Sepide Mofidifar]

 Hi Mark,
What I'm doing, is unbiased-molecular dynamics simulation. in similar to
the following reference that the interaction energy is calculated.
https://www.ncbi.nlm.nih.gov/pubmed/21545110
I think the calculation of interaction energy is favourable for these type
of studies, only I'm not sure that the summation of above options is the
right way to obtain interaction energy.

On 21 Feb 2018 14:42, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:

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