AMBER: correlation between PBTOT and GBTOT values in a MD trajectory

From: Giulio Rastelli <>
Date: Fri, 11 May 2007 16:47:39 +0200

Dear all,
we are analysing 2800 snapshots taken from a 14 ns MD simulation of a
protein-ligand complex in water using Amber9, and comparing MM-PBSA
(Amber PBSA, no Delphi) and MM-GBSA (igb=1) performance in binding free
energy prediction by analysing the free energy of each snapshot (i.e.
not printing only the average value)
We found that the PBTOT and GBTOT values of the 2800 snapshots correlate
well for complex,
receptor and ligand, while the complex - receptor - ligand (delta)
values of PBTOT and GBTOT do not correlate at all.

Complex: PBTOT vs GBTOT R2=0.88
                PBCAL vs GB R2=0.96

Receptor: PBTOT vs GBTOT R2=0.90
                PBCAL vs GB R2=0.97

Ligand PBTOT vs GBTOT R2=0.98
                PBCAL vs GB R2=0.90

Delta: PBTOT vs GBTOT R2=0.036
                PBCAL vs GB R2=0.41

I wonder if the lack of correlation of the binding free energy
differences (delta) is due to the uncertainties in the calculation of
the single contributions, which are sometimes high, or to the much lower
absolute values of the free energy contributions in delta with respect
to complex, receptor and ligand?

Average values:
Complex: GAS= -1817+/-128
                PBSUR= 128+/-1.8
                PBCAL= -4197+/-106
                GB= -4334+/-107

Receptor: GAS= -1790+/-129
                PBSUR= 130+/-1.8
                PBCAL= -4224+/-105
                GB= -4346+/-107

Ligand: GAS= 53+/-5
                PBSUR= 4.2+/-0.1
                PBCAL= -37.9+/-2
                GB= -34.3+/-1.9

Delta: GAS= -80+/-7.6
                PBSUR= -6.3+/-0.2
                PBCAL= 64.9+/-7.5
                GB= 46.5+/-6

Comments are really aprreciated.
Prof. Giulio Rastelli
Dipartimento di Scienze Farmaceutiche
Facolta' di Bioscienze e Biotecnologie
Universita' di Modena e Reggio Emilia
Via Campi 183
41100 Modena - ITALY
tel 0039-059-2055145
fax 0039-059-2055131
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Received on Sun May 13 2007 - 06:07:35 PDT
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