Table 7.
For differently minimized structures, the ΔΔGelec RMSD values are listed when corresponding sets across force fields are compared. The LEFT panels present the RMSD when bound/unbound states of monomeric chains were identical (‘Complex Minimized Only’) and the RIGHT panel presents the RMSD when monomers and their complexes were all individually minimized (non-identical bound/unbound state; ‘Complex + Chain Minimized’). NONMIN – protonated X-ray structures; MIN-500 – structures minimized for 500 CG steps and MIN-5000 – structures minimized for 5000 CG steps.
| Comparison Within Same Force-Field using ΔΔGelec Pearson correlation and (RMSD) (TRADITIONAL) | All RMSD values are in kcal/mol | ||||||||
|---|---|---|---|---|---|---|---|---|
| Identical Bound/Unbound states | Non-Identical Bound/Unbound states | |||||||
| CHARMM | AMBER | OPLS-AA | CHARMM | AMBER | OPLS-AA | |||
| NONMIN | CHARMM | 0 | 0.82 (40.71) |
0.82 (43.18) |
CHARMM | 0 | --- | --- |
| AMBER | 0 | 0.98 (15.47) |
AMBER | 0 | --- | |||
| OPLS-AA | 0 | OPLS-AA | 0 | |||||
| CHARMM | AMBER | OPLS-AA | CHARMM | AMBER | OPLS-AA | |||
| MIN-500 | CHARMM | 0 | 0.78 (50.81) |
0.80 (27.06) |
CHARMM | 0 | 0.85 (34.93) |
0.66 (41.21) |
| AMBER | 0 | 0.91 (40.51) |
AMBER | 0 | 0.61 (49.66) |
|||
| OPLS-AA | 0 | OPLS-AA | 0 | |||||
| CHARMM | AMBER | OPLS-AA | CHARMM | AMBER | OPLS-AA | |||
| MIN-5000 | CHARMM | 0 | 0.74 (58.01) |
0.77 (29.24) |
CHARMM | 0 | 0.84 (40.12) |
0.58 (50.40) |
| AMBER | 0 | 0.91 (41.43) |
AMBER | 0 | 0.56 (55.88) |
|||
| OPLS-AA | 0 | OPLS-AA | 0 | |||||
For the NONMIN set, the Bound/Unbound states of the monomers are the same. Hence, the corresponding fields do not contain any values. The change occurs only after minimization (MIN-500/5000).