Table 6.
The effects of solute dielectric constant (epsin) upon the performance of MMPBSA. All calculations were conducted with the new nonpolar solvent model (inp=2) and the default SES surface (sasopt=0) as in Table 1, but with all three tested dielectric constant options. The RMSD’s of ΔΔG are in kcal/mol.
| Dielectric constant |
RMSD | R | Slope | |||
|---|---|---|---|---|---|---|
| Median | Range | Median | Range | Median | Range | |
| 1 | 5.82 | 4.28–7.78 | 0.20 | 0.18–0.86 | 0.05 | −0.16–0.34 |
| 4 | 3.28 | 1.94–4.26 | 0.60 | 0.30–0.86 | 0.31 | 0.23–0.42 |
| 20 | 3.46 | 1.79–4.88 | 0.66 | 0.46–0.86 | 0.32 | 0.27–0.39 |