Table 7.
Convergence of simulated free energy versus accuracy: comparison of MMPBSA results using converged free energies versus those using just the first nanosecond. All calculations were conducted with the DEN surface (sasopt=2) and optimized radius set (radiopt=1) as in Table 5 for efficiency. The RMSD’s of ΔΔG are in kcal/mol. See Figure 3 for the free energy convergence analysis.
| Systems | 10ns | 1ns | ||||
|---|---|---|---|---|---|---|
| RMSD | R | Slope | RMSD | R | Slope | |
| CDK+PKA | 3.65 | 0.72 | 0.30 | 3.51 | 0.73 | 0.29 |
| glucosidase | 1.77 | 0.47 | 0.38 | 1.70 | 0.43 | 0.34 |
| thrombin | 4.58 | 0.86 | 0.40 | 4.46 | 0.88 | 0.41 |
| trypsin | 3.10 | 0.67 | 0.37 | 3.25 | 0.66 | 0.36 |
| urokinase | 2.23 | 0.67 | 0.47 | 2.17 | 0.60 | 0.43 |
| Factor Xa | 3.00 | 0.70 | 0.30 | 2.85 | 0.71 | 0.31 |