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

[Mark Abraham]

Hi,

Their method for estimating the free energy of binding as an interaction
energy (one of many published, hint, hint) doesn't use any of those terms
from gmx energy, and there's good reasons for that. I suggest you read a
bit and decide what you want to do, rather than hoping you can add up
quantities you already calculated to compute something whose definition is
unclear until you choose one.

Mark

On Wed, Feb 21, 2018 at 1:13 PM Sepide Mofidifar <s.mofidifar at gmail.com>
wrote:

>  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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