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. Author manuscript; available in PMC: 2013 Aug 30.
Published in final edited form as: J Chem Inf Model. 2012 Jul 6;52(7):1821–1832. doi: 10.1021/ci3000997

Table 6.

Comparison of binding free energies (kcal/mol) calculated with reduced systems (GSBP/SSBP) to those with fully solvated systems (periodic boundary condition, PBC) for the X-ray MDM2/X structuresa

expt GSBP/SSBP
PBC
Run 6–10 Run 6–10 Run 11–20 Run 21–30
T-1 −9.41 −14.10 ± 2.64 −9.90 ± 2.45 −11.45 ± 1.93 −12.16 ± 1.71
T-2 −9.74 −21.20 ± 0.90 −11.04 ± 0.77 −12.40 ± 2.63 −12.04 ± 0.45
T-3 −8.11 −18.66 ± 1.72 −13.90 ± 0.56 −13.92 ± 1.52 −14.26 ± 0.80
T-4 −8.29 −16.31 ± 2.56 −10.95 ± 0.86 −13.01 ± 0.72 −13.02 ± 1.46
X-1 −6.81 −7.52 ± 3.67 −5.18 ± 1.37 −4.61 ± 2.67 −6.91 ± 2.51
a

The free energies and the errors are the averages and the standard deviations of the continuous FEP/MD cycles, respectively. For example, the free energies on the “Run 6-10” column are the average of five runs from cycle 6 to 10.