TABLE 2.
A summary of the parameterization protocol used for the development of four carbohydrate force fields reviewed
| CHARMM | GLYCAM06 | GROMOS-45A4 | OPLS-AA-SEI | |
|---|---|---|---|---|
| Valence terms | ||||
| Equilibrium bond lengths (r) and angles (θ) | Chosen to reproduce crystal internal and unit-cell geometries | Chosen to reproduce neutron-diffraction geometries | GROMOS-45A3 | OPLS-AA |
| Force constants kb/kθ | Fit to QM data | Fit to QM data | GROMOS-45A3 | OPLS-AA |
|
| ||||
| Torsion terms | Fit to QM rotational energy curves | Fit to QM rotational energy curves | Fit to QM rotational energy curves | Fit to QM rotational energy curves |
|
| ||||
| Partial charges | Empirically fit for carbohydrate fragments, and refined to reproduce: QM solute–water Eint, and experimental Vm of carbohydrate solutions | QM RESP fit and ensemble averaged over multiple conformations. RESP scaling to reproduce crystal unit-cell geometries | QM RESP fit with averaging over atom types | OPLS-AA (empirically fit to reproduce heat of vaporization and densities of pure liquids) |
|
| ||||
| vdW terms | CHARMM22 | AMBER PARM94 | GROMOS-45A3 | OPLS-AA |
|
| ||||
| 1,4 scaling (Elec/vdW) | No/no | No/no | No/no | Yes/yes |
|
| ||||
| Unique charge sets for α- and β-anomers | No | Yes | No | No |
|
| ||||
| Unique charges on each atom | No | Yes | No | No |
|
| ||||
| Unique atom types for α- and β-anomers | Yes | No | Yes | Yes |