Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data

Oliver F. Lange; David van der Spoel; Bert L. de Groot

doi:10.1016/j.bpj.2010.04.062

Table 1

Quality measurement of R-free and correlation coefficient r for ^3hJ couplings across hydrogen bonds predicted with various force fields with PME electrostatics

	R_H–bond(gb3)	r_H–bond(gb3)	R_H–bond(ubi)	r_H–bond(ubi)
AMBER03	0.29	0.58	0.26	0.55
AMBER99sb	0.16	0.85	0.19	0.80
OPLS/AA	0.28	0.67	0.29	0.64
CHARMM22	0.26	0.68	0.23	0.70
g96_43a1	0.30	0.45	0.29	0.36
g96_53a6	0.31	0.2	0.28	0.39
2k39			0.19	0.81
2igd	0.20	0.85
1igd	0.30	0.81
AMBER03_50ns	0.25	0.69	0.24	0.58
AMBER99sb_50ns	0.16	0.85	0.18	0.81
OPLSAA_50ns	0.26	0.69	0.26	0.76

The last three rows refer to predictions based on 20 × 50 ns MD simulations rather than a single 1000 ns simulation. A graphical version of this table is shown in Fig. S3 and includes values for cut-off and reaction-field simulations.