You can refer to the article below.
http://pubs.acs.org/doi/abs/10.1021/ct060037v
On Wed, Nov 28, 2012 at 1:05 PM, manikanthan bhavaraju <
manikanthanbhavaraju.gmail.com> wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best,
InSuk Joung
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 28 2012 - 10:30:02 PST
