[AMBER] MMPBSA binding energy

From: Eliac Brown <eliacbrown.yahoo.com>
Date: Wed, 29 Dec 2010 17:11:44 -0800 (PST)

MMPBSA binding energy is given by:
dG = Gcomplex - Gligand - Greceptor
We always use single trajectory approach to calculate G from each species where it is faster than the 2- or 3- trajectory approach.
Here is my question:
If we calculated the ddG for different inhibitors binding with a certain protein, so:
ddG= (Gcomplex1 -Gcomplex2) - (Gligand1-Gligand2) - (Greceptor1-Greceptor2)
because we study the inhibition of some ligands with the same protein, so we could consider:
Greceptor1 = G receptor2 (as I believe it is the case in 3-trajectory approach)
ddG= (Gcomplex1 -Gcomplex2) - (Gligand1-Gligand2)
So, why when I used the later equation I got a horrible results using single trajectory? I would expect to get the same results.
Any hint would be appreciated.
Happy New Year to all


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Received on Wed Dec 29 2010 - 17:30:02 PST
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