Name
Title | ||
|---|---|---|
On the force field optimisation of $$\beta$$ β -lactam cores using the force field Toolkit |
Abstract | ||
|---|---|---|
When employing molecular dynamics (MD) simulations for computer-aided drug design, the quality of the used force fields is highly important. Here we present reparametrisations of the force fields for the core molecules from 9 different
$$\beta$$
-lactam classes, for which we utilized the force field Toolkit and Gaussian calculations. We focus on the parametrisation of the dihedral angles, with the goal of reproducing the optimised quantum geometry in MD simulations. Parameters taken from CGenFF turn out to be a good initial guess for the multiplicity of each dihedral angle, but the key to a successful parametrisation is found to lie in the phase shifts. Based on the optimised quantum geometry, we come up with a strategy for predicting the phase shifts prior to the dihedral potential fitting. This allows us to successfully parameterise 8 out of the 11 molecules studied here, while the remaining 3 molecules can also be parameterised with small adjustments. Our work highlights the importance of predicting the dihedral phase shifts in the ligand parametrisation protocol, and provides a simple yet valuable strategy for improving the process of parameterising force fields of drug-like molecules. |
Year | DOI | Venue |
|---|---|---|
2022 | 10.1007/s10822-022-00464-3 | Journal of Computer-Aided Molecular Design |
Keywords | DocType | Volume |
Ligand force field parametrisation, ffTK, Dihedral phase shifts prediction, CGenFF | Journal | 36 |
Issue | ISSN | Citations |
7 | 0920-654X | 0 |
PageRank | References | Authors |
0.34 | 6 | 7 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Qiyang Wu | 1 | 0 | 0.34 |
| Tianyang Huang | 2 | 0 | 0.34 |
| Songyan Xia | 3 | 0 | 0.34 |
| Frank Otto | 4 | 0 | 0.34 |
| Tzong-Yi Lee | 5 | 0 | 0.34 |
| Hsien-Da Huang | 6 | 835 | 63.83 |
| Ying-Chih Chiang | 7 | 0 | 0.34 |