Table 11.
Traditional method | Multiple Independent Sampling | ||
---|---|---|---|
a. Accuracy of Implicit Solvent Methods | QM/MM-GBSA > MM-GBSA > MM-PBSA | QM/MM-GBSA ≈ MM-GBSA > MM-PBSA | |
MM-GBSA & QM/MM-GBSA | |||
Traditional method | Multiple Independent Sampling | ||
b. Accuracy of GB Methods | GBNeck2 > GBHTC >= GBOBC = GBOBC2 > GBNeck | Differences are minimized | |
MM-PBSA | |||
Traditional method | Multiple Independent Sampling | ||
c. Accuracy of Radii Settings | bondi = mbondi2 ≈ mbondi > PARSE | Differences are minimized | |
MM-GBSA & QM/MM-GBSA | |||
GB Method Names | AMBER igb flag | Traditional method | Multiple Independent Sampling |
GBHCT | 1 | bondi = mbondi2 ≈ mbondia | Differences are minimized |
GBOBC | 2 | bondia = mbondi2a ≈ mbondi | Differences are minimized |
GBOBC2 | 5 | bondia = mbondi2a >≈b mbondi | Differences are minimized |
GBNeck | 7 | mbondi2a,c ≈ bondi | Differences are minimized |
GBNeck2 | 8 | mbondi2a,d ≈ bondi | Differences are minimized |
QM/MM-GBSA | |||
d. Accuracy of PM Hamiltonians | PM3 > AM1 > PM6 |
AMBER user manual recommended radii sets for the GB methods.
In MM-GBSA and GBOBC2: bondia = mbondi2a > mbondi. In QM/MM-GBSA and GBOBC2: bondia = mbondi2a ≈ mbondi
bondi might also work, but it might cause instability in the native peptide REMD type of simulation.
mbondi3 is recommended in the MD/REMD type of simulation.