. Author manuscript; available in PMC: 2013 Apr 10.

Published in final edited form as: J Chem Theory Comput. 2012 Jan 2;8(4):1314–1324. doi: 10.1021/ct200812y

Table 5.

Relative binding free energies from alchemical perturbation calculations (kcal/mol). In the BAR procedure the simulation was performed using an induced-dipole convergence of 0.01 D per atom, and the free energy was evaluated with a tighter convergence (10⁻⁶) using eqn (3). The reweighting BAR introduces a rigorous reweighting due to the different polarization convergence based on eqn (4).

	BAR (eqn.(3))			Reweighting BAR (eqn.(4))			BAR with Zn charge set to 0			BAR without polarization by Zn²⁺			Experiment Results

	ΔG_lig-wat	ΔG_lig-pro	ΔΔG	ΔG_lig-wat	ΔG_lig-pro	ΔΔG	ΔG_lig-wat	ΔG_lig-pro	ΔΔG	ΔG_lig-wat	ΔG_lig-pro	ΔΔG	ΔΔG_expr^a
4→3	4.14	5.52	1.38	4.14	5.55	1.41	4.14	5.82	1.68	4.14	5.29	1.15	1.30
4→2	11.94	13.45	1.51	13.47	15.15	1.68	11.94	15.01	3.07	11.94	13.02	1.08	2.32
2→1	−10.07	−9.36	0.71	−9.77	−9.30	0.46	−10.07	−5.52	4.55	−10.07	−10.85	−0.62	1.66

Ref ¹⁰⁰.