[gmx-users] Binding Energy to Binding affinity (Kd)
Du Jiangfeng (BIOCH)
j.du at maastrichtuniversity.nl
Mon Oct 1 10:36:10 CEST 2012
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?
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 appreciate any reply.
Jiangfeng Du, PhD Student
Cardiovascular Research Institute Maastricht
Department of Biochemistry
P.O. Box 616
6200 MD Maastricht
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