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?
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.
Thanks,
Jiangfeng Du, PhD Student
Cardiovascular Research Institute Maastricht
Department of Biochemistry
P.O. Box 616
Mobile: +31-681741859
FAX: +31-43-3884159
6200 MD Maastricht
The Netherlands--
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