[gmx-users] binding free energy

[Billy Williams-Noonan]

You would want to perturb your amino acid in both the free (unbound) and
complex (bound) aqueous states.

Then if you subtract the free energy change from perturbing the free
ligand, from that of perturbing the bound ligand, you should close the
non-physical thermodynamic cycle and get a binding free energy.

But you will need to make sure everything in your simulation is
parameterised properly to get an accurate value.  You will also need to
make sure you have sufficient sampling time and lambda states.

Good luck!

Billy

On Tuesday, 5 July 2016, Alexander Alexander <alexanderwien2k at gmail.com
<javascript:_e(%7B%7D,'cvml','alexanderwien2k at gmail.com');>> wrote:

> Dear gromacs user,
>
> I was wondering if anybody has any experience with binding free energy
> calculation of a molecule (here amino acid) into a solid surface in aqueous
> solution using alchemical analysis?
>
> I have already tried successfully the tutorial of methane solvation free
> energy in water and some other examples, but looks all of them are
> solvation free energy and not binding free energy!
>
> Thanks.
> Regards,
> Alex
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