. 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 11.

Summary of the Effect of Parameters on Predictive Power

		Traditional method	Multiple Independent Sampling
a. Accuracy of Implicit Solvent Methods		QM/MM-GBSA > MM-GBSA > MM-PBSA	QM/MM-GBSA ≈ MM-GBSA > MM-PBSA
		MM-GBSA & QM/MM-GBSA
		Traditional method	Multiple Independent Sampling
b. Accuracy of GB Methods		GB^Neck2 > GB^HTC >= GB^OBC = GB^OBC2 > GB^Neck	Differences are minimized
		MM-PBSA
		Traditional method	Multiple Independent Sampling
c. Accuracy of Radii Settings		bondi = mbondi2 ≈ mbondi > PARSE	Differences are minimized
		MM-GBSA & QM/MM-GBSA
GB Method Names	AMBER igb flag	Traditional method	Multiple Independent Sampling
GB^HCT	1	bondi = mbondi2 ≈ mbondi^a	Differences are minimized
GB^OBC	2	bondi^a = mbondi2^a ≈ mbondi	Differences are minimized
GB^OBC2	5	bondi^a = mbondi2^a >≈^b mbondi	Differences are minimized
GB^Neck	7	mbondi2^a,c ≈ bondi	Differences are minimized
GB^Neck2	8	mbondi2^a,d ≈ bondi	Differences are minimized
		QM/MM-GBSA
d. Accuracy of PM Hamiltonians		PM3 > AM1 > PM6

AMBER user manual recommended radii sets for the GB methods.

In MM-GBSA and GB^OBC2: bondi^a = mbondi2^a > mbondi. In QM/MM-GBSA and GB^OBC2: bondi^a = mbondi2^a ≈ mbondi

bondi might also work, but it might cause instability in the native peptide REMD type of simulation.

mbondi3 is recommended in the MD/REMD type of simulation.