[gmx-users] Binding Energy to Binding affinity (Kd)

Justin Lemkul jalemkul at vt.edu
Mon Oct 1 14:46:23 CEST 2012

On 10/1/12 4:36 AM, Du Jiangfeng (BIOCH) wrote:
> Dear Everyone,
> I have two questions about the conversion of binding energy to binding
> affinity.
> I predicted the binding energy of a protein-membrane complex by umbrella
> sampling (based on Justin's tutorial). After sampling, the binding energy
> should be the substract of (min-max) PMF. I have repeated the simulation 12
> times, and then I have done umbrella samplings also 12 times, then got 12
> binding energies which varies from -200 Kcal/mol to -100kcal/mol, does the
> value vary too much? or is it reasonable since the simulation results can be
> different? Are those values too huge?

Without an explanation of how long your windows are and what the error estimate 
for each replicate is, it is impossible to answer this question.

> When I tried to convert the binding energy to Kd by the formula
> deltaG=-RTlnK, I am frustrated by the kd value. If the binding energy is
> -100kcal/mol, the kd is calculated as 3.35e-59  μM.  The kd is 1.77e-126  μM
> when binding energy is -200kcal/mol. This is impossible.  But what is going
> wrong?

I think you are doing your calculations incorrectly (I obtain your values when 
using units of kcal/mol for dG but kJ/mol-K for the gas constant - note the 
mismatch), but even when done properly, the values are still unreasonable.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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