. 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 3.

The coefficient of determination of Experimental and Predicted Binding Free Energies of Different MD Trajectory Lengths and Radii Sets in QM-MM/GBSA Calculations using the PM3 Hamiltonian.^a

Radii Sets	GB	R²_0.25ns^a	R²_0.5ns	R²_0.75ns	R²_1ns	R²_2ns	R²_3ns	R²_4ns	R²_5ns	R²_6ns
bondi	GB^HCT	0.78	0.81	0.78	0.73	0.64	0.58	0.53	0.52	0.54
mbondi	GB^HCT	0.76	0.79	0.75	0.69	0.59	0.56	0.54	0.55	0.57
mbondi2	GB^HCT	0.78	0.81	0.78	0.73	0.64	0.58	0.54	0.52	0.54

bondi	GB^OBC	0.76	0.79	0.76	0.72	0.64	0.6	0.56	0.54	0.56
mbondi	GB^OBC	0.72	0.75	0.71	0.67	0.57	0.55	0.53	0.54	0.56
mbondi2	GB^OBC	0.76	0.79	0.76	0.71	0.63	0.59	0.55	0.53	0.55

bondi	GB^OBC2	0.75	0.79	0.75	0.71	0.62	0.56	0.51	0.49	0.51
mbondi	GB^OBC2	0.72	0.75	0.71	0.64	0.51	0.47	0.44	0.44	0.46
mbondi2	GB^OBC2	0.75	0.78	0.75	0.69	0.59	0.54	0.49	0.47	0.49

bondi	GB^Neck	0.73	0.73	0.69	0.64	0.52	0.46	0.4	0.39	0.42
mbondi2	GB^Neck	0.72	0.72	0.68	0.63	0.51	0.44	0.38	0.37	0.4

bondi	GB^Neck2	0.62	0.66	0.62	0.65	0.69	0.76	0.79	0.82	0.86
mbondi2	GB^Neck2	0.64	0.67	0.64	0.67	0.7	0.78	0.81	0.83	0.88

R²_n: “R²” stands for coefficient of determination in the QM-MM/GBSA calculation. Here 100, 400, 1200, 2400 MD simulation frames were evenly extracted from one 0.25, 1, 3, 6 ns MD simulation trajectories, respectively.