Skip to main content
. Author manuscript; available in PMC: 2016 Sep 30.
Published in final edited form as: J Comput Chem. 2015 Jul 27;36(25):1859–1873. doi: 10.1002/jcc.24011

Table 7.

Summary of Impact of Entropy on Predicted Binding Free Energies of MD Trajectories of Different Lengths and Radii Sets in MM/GBSA and QM-MM/GBSA Calculations

MM/GBSA QM-MM/GBSA
1 2 3 4 5 6 7 8 9 10 11 12
Radii Sets GB R26nsa,b R26nsc R26nsd R26nse Radii Sets GB R26nsa,b R26nsc R26nsd R26nse
bondi GBHCT 0.41 0.24 0.37 0.14 bondi GBHCT 0.54 0.52 0.54 0.48
mbondi GBHCT 0.44 0.3 0.42 0.22 mbondi GBHCT 0.57 0.59 0.59 0.58
mbondi2 GBHCT 0.41 0.24 0.37 0.14 mbondi2 GBHCT 0.54 0.54 0.54 0.50
bondi GBOBC 0.38 0.12 0.31 0.04 bondi GBOBC 0.56 0.51 0.56 0.41
mbondi GBOBC 0.36 0.12 0.30 0.04 mbondi GBOBC 0.56 0.54 0.57 0.49
mbondi2 GBOBC 0.36 0.12 0.29 0.03 mbondi2 GBOBC 0.55 0.52 0.55 0.43
bondi GBOBC2 0.36 0.13 0.27 0.04 bondi GBOBC2 0.51 0.45 0.49 0.36
mbondi GBOBC2 0.24 0.05 0.16 0.00 mbondi GBOBC2 0.46 0.42 0.43 0.35
mbondi2 GBOBC2 0.32 0.1 0.23 0.02 mbondi2 GBOBC2 0.49 0.45 0.46 0.35
bondi GBNeck 0.16 0.00 0.07 0.02 bondi GBNeck 0.42 0.28 0.35 0.14
mbondi2 GBNeck 0.15 0.00 0.06 0.02 mbondi2 GBNeck 0.4 0.28 0.34 0.15
bondi GBNeck2 0.5 0.07 0.42 0.06 bondi GBNeck2 0.86 0.47 0.75 0.42
mbondi2 GBNeck2 0.51 0.07 0.43 0.07 mbondi2 GBNeck2 0.88 0.52 0.76 0.46
a

R2n: “R2” stands for coefficient of determination in the MM/PBSA calculation. Here 2,400 MD simulation frames were evenly extracted from 6 ns MD simulation trajectories.

b

2,400 frames calculated enthalpy & no calculated entropy

c

2,400 frames calculated enthalpy & 48 frames calculated entropy

d

48 frames calculated enthalpy & no calculated entropy

e

48 frames calculated enthalpy & 48 frames calculated entropy