Table 5.

The effects of molecular surface definitions (sasopt) upon the performance of MMPBSA. Both the default Amber atomic radius definition (radiopt=0) and optimized atomic radius (radiopt=1) were used in the analysis. The testing conditions are otherwise the same as those in Table 1 but with all six tested combinations of surface and radius options. Here the solvent probe is set to the optimized value (dprob=0.6) in SES and DEN as reported in our previous studies^{26, 30}. For VDW dprob=0.0 by definition. The RMSD’s of ΔΔG are in kcal/mol.

Setting	RMSD		R		Slope
	Median	Range	Median	Range	Median	Range
SES, radiopt=0	3.05	1.54–4.39	0.66	0.47–0.86	0.38	0.26–0.42
VDW, radiopt=0	3.22	1.67–4.88	0.69	0.54–0.87	0.34	0.25–0.40
DEN, radiopt=0	2.94	1.65–3.99	0.66	0.40–0.87	0.35	0.26–0.44
SES, radiopt=1	3.11	1.77–4.89	0.70	0.59–0.87	0.37	0.27–0.41
VDW, radiopt=1	3.30	1.73–5.05	0.69	0.53–0.86	0.35	0.24–0.41
DEN, radiopt=1	3.05	1.70–4.46	0.69	0.43–0.88	0.35	0.29–0.43