[gmx-users] Hypericin dimer affinity

[Justin A. Lemkul]

On 4/24/12 7:47 AM, Hovakim Grabski wrote:
> Dear Gromacs users,
>
> I set up a simulation of 4 Hypericin molecules for 5 ns.
> 2 of them formed a dimer.
> Is there any way to find the dissociation constant Kd and bond energy of Hypericin ?

Umbrella sampling is one method from which you might be able to determine the 
binding free energy.  You could then back-calculate a Kd value from this free 
energy.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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