AMBER Archive (2006)

Subject: Re: AMBER: modeling of ligand concentrations

From: David A. Case (case_at_scripps.edu)
Date: Mon Oct 16 2006 - 17:24:34 CDT

On Mon, Oct 16, 2006, Sean Rathlef wrote:
>
> I have a ligand (L) and a receptor (R). I am forming a complex LR, and want
> to model this in NPT. The energy levels of L + R and also of complex RL is
> going to depend on the standard state selection of [L]. Hence, if I model a
> single molecule of L and a single molecule or R, the relative energy will
> not take into consideration the concentration of L.

But the *free* energy estimates will know about standard states. Basically
the standard state of the the ligand (by default, 1M) is included in its
translational entropy (ditto for the receptor and the complex). So, the
mm-pbsa procedure would naturally account for ligand concentration.

Note that this implies the assumption of an ideal solution. Deviations from
ideality (such that concentration and activity are not the same) are certainly
possible, but are rarely considered in actual calculations.

...hope this helps...dac

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