[gmx-users] Sampling a weak ligand

[Александр Лашков]

May be you should add intermolecular interaction as is in FEP calculation
for protein-ligand complex.
Alexander Lashkov

вт, 24 дек. 2019 г., 3:05 Raphaël Robidas <raphaelrobidas at gmail.com>:

> Hello all,
>
> I am running free energy perturbation calculations to determine the
> absolute affinity of a weak ligand. To prevent dissociation and increase
> sampling, the first few lambda states introduce a harmonic restraint via
> the intermolecular interactions feature. The problem is that my ligand
> dissociates in the first state, which has no restraint at all. Is there a
> technique to still get an accurate value? I plan on running a longer
> simulation for the first state in order to sample more the bound state, but
> I hope that there is a smarter way!
>
> Thanks and happy holidays!
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