On Thu, 2014-04-24 at 13:46 +0300, Fabian Glaser wrote:
> Hi,
>
> 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
OK.
> 2) Run MD in vacuum
Don't do this.
> or water
Do this instead.
> 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)?
> Is the correct approach?
> Is there any paper on that? I did not found any, but I am not an expert in the matter.
>
> Please note there is no protein involved here.... only two ligands.
MM/PBSA will be of little use to you. An "interaction free energy" is
difficult to compute using just energies (and don't forget, their
interactions are strongly water-mediated so a simple pairwise summation
between the molecules is unlikely to yield much insight).
You can generate a general PMF using a radial distribution function, but
I'm not sure exactly what you are trying to accomplish. Also don't
forget that your free energy depends on your state (that is, the
concentrations of each species), so it's important to specify what you
want as specifically as possible (rather than just say "an interaction
free energy"). It'll be easier to design an experiment or metric to
measure what you want that way.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Apr 24 2014 - 05:00:03 PDT
