On Thu, Apr 24, 2014, Fabian Glaser wrote:
>
> I am interested to calculate the free energy of interaction on many
> frames of MD for two drug like molecules, I plan the following:
>
> 1) Prepare the molecules with antechamber
> 2) Run MD in vacuum or water
> 3) Calculate MM-PBSA as you did for a protein-ligand on
> http://ambermd.org/tutorials/advanced/tutorial3/
>
> Is that a good idea for two copies of drug molecules (e.g. RITONAVIR)?
In principle, it doesn't matter what the "ligand" and "receptor" are: they
could both be drug molecules. But is seems likely that the two drug molecules
may move apart from each other during the MD simulation, which will lead
to a very small free energy of interaction. But perhaps the molecule is
known to dimerize(?)
....dac
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Received on Thu Apr 24 2014 - 05:30:03 PDT
