Tutorial-l Mailing List

From: Hossein Mohammadiarani (hm2006_at_wildcats.unh.edu)
Date: Thu Jan 26 2017 - 12:00:13 CST

Hello

I am doing "Protein:ligand standard binding free energies tutorial". In the Geometrical route calculation there is a term that should be calculated analytically (S*). The value of S* is given in the tutorial (S? = 17.15 A? ^2, page 21) which is calculated based on the following formulas and constants:

S*= (r*)^2 ? d? sin ? ? d? e(-?*ua)

In which:

r*=35 (A? )

? range = 0 to 180

? range = 0 to 360

?= 1.67 (mol/kcal)

ua=1/2*0.1*(?-40).^2 + 1/2*0.1*(?-(-80)).^2;

My calculation shows that S* is a very small number (let say zero, S*=0).

Do you know where is my possible mistake in the mentioned formulas and coefficients?

Thanks

Hossein

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