[gmx-users] Umbrella Sampling result

[Alexander Law]

Great thanks, I got a value from the PMF curve as -18.3 kcal/mol (-76600 J/mol) and I did the calculation and I got an absurd result:

Kd = e^(∆G/(RT))

Kd= e^(-76600/(83144*298.15)) = 3.8032908e-14 M

The real value is 0.76 uM...

Where have I gone wrong?

Many Thanks
Alex
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Warren Gallin [wgallin at ualberta.ca]
Sent: Monday, March 02, 2015 11:38 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling result

The equation you refer to is:

∆G=RTln(Kd)  [The extra factor in the Wikipedia entry is unnecessary, since  there is no actual unit for the “concentration terms” ; the relevant number is activity, which is dimensionless and which approaches the numerical value of the concentration when the concentrations are small.]

So there is no concentration term to consider.

Warren Gallin

> On Mar 1, 2015, at 2:27 PM, Alexander Law <alexander.law at pg.canterbury.ac.nz> wrote:
>
> Dear gmx-users
>
> Is it possible to produce a valid dissociation constant value from gibbs free energy value produced from umbrella sampling?
>
> The equation is given at the bottom of the this wikipedia page:
>
> http://en.wikipedia.org/wiki/Binding_constant
>
> Is the concentration term vital since the ligand and the protein at a 1:1 mol ratio?
>
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