Table 6.

For each force field, the ΔΔG_elec RMSD for the various pairs of differently minimized structures are shown. The LEFT panels present the RMSD when bound/unbound states of monomeric chains were identical (‘Complex Minimized Only’) and the RIGHT panel presents the RMSD when monomers and their complexes were all individually minimized (non-identical bound/unbound state; ‘Complex + Chain Minimized’). NONMIN – protonated X-ray structures; MIN-500 – structures minimized for 500 CG steps and MIN-5000 – structures minimized for 5000 CG steps.

Comparison Within Same Force-Field using ΔΔGelec Pearson correlation and (RMSD) (TRADITIONAL) | All RMSD values are in kcal/mol
Identical Bound/Unbound states					Non-Identical Bound/Unbound states
		NONMIN	MIN-500	MIN-5000		NONMIN	MIN-500	MIN-5000
CHARMM	NONMIN	0	0.95 (28.59)	0.91 (38.54)	NONMIN	0	0.91 (30.73)	0.91 (35.63)
	MIN-500		0	0.97 (12.88)	MIN-500		0	0.94 (15.51)
	MIN-5000			0	MIN-5000			0
		NONMIN	MIN-500	MIN-5000		NONMIN	MIN-500	MIN-5000
AMBER	NONMIN	0	0.99 (10.16)	0.98 (10.57)	NONMIN	0	0.79 (42.59)	0.79 (42.53)
	MIN-500		0	0.99 (2.94)	MIN-500		0	0.93 (19.95)
	MIN-5000			0	MIN-5000			0
		NONMIN	MIN-500	MIN-5000		NONMIN	MIN-500	MIN-5000
OPLS-AA	NONMIN	0	0.92 (46.62)	0.91 (48.21)	NONMIN	0	0.51 (68.33)	0.47 (71.85)
	MIN-500		0	0.99 (4.47)	MIN-500		0	0.79 (35.38)
	MIN-5000			0	MIN-5000			0