Dear Amber Developers,
I have performed TI calculations on protein+ligand system using ff99
and amber8. Now I am interested to compare my results with the
experimental values. After some literature review I have found that
people have experimentally determined dissociation constants. I have
few doubts about comparing TI results with the experimental values.
I have calculated the experimental free energy for protein-ligand --->
protein + ligand (3.9 kcal/mol). The TI's deltaA value is 9.2
kcal/mol
Note: TI's binding deltaA was -9.2 kcal/mol
I am assuming that the experiment deltaG as deltaG(std). In order to
compare TI value with the experimental value I have to calculate
deltaG(std).
deltaG (std) = deltaG - RTlnK
What information I have to extract from the TI simulations to
calculate K value? or What terms should be considered ?
If my assumption is wrong please correct me. Is there any article
that I can refer to ?
Thanks,
mani
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Received on Wed Nov 28 2012 - 10:30:02 PST
