On Sat, Apr 26, 2014 at 10:12 AM, James Starlight <jmsstarlight.gmail.com>wrote:
> Jason,
>
> works perfect.
> Using igb=2, saltcon=0.150,
> I've obtained below results for the high affinity agonist of my membrane
> receptor (here protein's entropy had not been taken into account):
>
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
> -------------------------------------------------------------------------------
> VDWAALS -49.2645 3.5945
> 0.3595
> EEL -139.6615 6.8852
> 0.6885
> EGB 136.3443 5.7616
> 0.5762
> ESURF -7.5376 0.1172
> 0.0117
>
> DELTA G gas -188.9260 7.1462
> 0.7146
> DELTA G solv 128.8067 5.7253
> 0.5725
>
> DELTA TOTAL -60.1193 3.6655
> 0.3665
>
> It's looks very good. But why EEL and EGB are so differs in sights?
>
That is the nature of those potential terms -- they are competing effects.
I would suggest familiarizing yourself with the theory of solvation and
the GB equations if you want deeper insight as such compensatory behavior
is very common. Also, if you look at the thermodynamic cycle and analyze
what is happening on the microscopic scale for each step it should make
sense. (Think about what the solvent molecules are doing and how each
component of the system interacts with each other and how those
interactions change along each step of the reaction coordinate).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Apr 26 2014 - 07:30:03 PDT
