Calculations of Absolute Solvation Free Energies with Transformato─Application to the FreeSolv Database Using the CGenFF Force Field

J Karwounopoulos, Å Kaupang, M Wieder… - Journal of Chemical …, 2023 - ACS Publications
… for the computational prediction of transfer free energies, ie, … charge models together with
the OPLS-AA force field. (34) … tend to be too positive, so the LRC on average improves the …

MLSolvA: solvation free energy prediction from pairwise atomistic interactions by machine learning

H Lim, YJ Jung - Journal of Cheminformatics, 2021 - Springer
solvation processes and is capable of strengthening various … Color shading depicts the
predicted hydration free energies … to low and high hydration free energy cases, respectively. The …

CHARMM-GUI free energy calculator for absolute and relative ligand solvation and binding free energy simulations

S Kim, H Oshima, H Zhang, NR Kern, S Re… - Journal of chemical …, 2020 - ACS Publications
free energy simulations have long been utilized to predict … of Free Energy Calculator,
which will be improved in the future. … for FEP calculations, using different ligand force fields …

PyAutoFEP: An automated free energy perturbation workflow for GROMACS integrating enhanced sampling methods

L Carvalho Martins, EA Cino… - Journal of Chemical …, 2021 - ACS Publications
improved predictions compared to CHARMM36m. Finally, we estimated the probability of
finding a molecule 1 pK i better than a lead when using … RMSEc, our predictions using OPLS-AA…

Prediction of octanol-water partition coefficients for the SAMPL6- molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force …

S Fan, BI Iorga, O Beckstein - Journal of computer-aided molecular design, 2020 - Springer
Absolute solvation free energies were computed by … protocol using 5-ns windowed alchemical
free energy perturbation (FEP) … improved the RMSE of the GAFF \(\log P_{ow}\) predictions

[HTML][HTML] A fast and high-quality charge model for the next generation general AMBER force field

X He, VH Man, W Yang, TS Lee, J Wang - The Journal of Chemical …, 2020 - pubs.aip.org
… excellent performance in the solvation free energy (SFE) … used for the absolute or relative
protein-ligand binding free energy … a feasible way to greatly improve the performance of GAFF2/…

Hybrid alchemical free energy/machine-learning methodology for the computation of hydration free energies

J Scheen, W Wu, ASJS Mey, P Tosco… - Journal of Chemical …, 2020 - ACS Publications
hydration free energies with the OPLS hydration free energies (Pearson r 0.95, mean absolute
… QM derived corrections to improve GAFF hydration free energies reported in submission …

Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules

A Chakravorty, A Hussain, LF Cervantes… - Journal of Chemical …, 2024 - ACS Publications
… with other contemporaneous ones like OPLS. Here, we analyze … the absolute hydration free
energy of over 600 small molecules, … The improved MAE and RMSE values (compared to our …

Assessment of GAFF and OPLS force fields for urea: crystal and aqueous solution properties

S Anker, D McKechnie, P Mulheran, J Sefcik… - Crystal Growth & …, 2023 - ACS Publications
… structural correlations, diffusion and solvation free energy; … the crystal and solution properties
predicted using these force … , there are significant and increasing fluctuations of the crystal …

… dynamics simulations and computing hydration free energies on the B3LYP-D3 (BJ) potential energy surface with adaptive force matching: a benchmark study with …

D Zheng, F Wang - ACS Physical Chemistry Au, 2021 - ACS Publications
… The solute–water cross terms are iteratively improved during the AFM … predict a trend similar
to experiments with the isobutanol absolute HFE smaller by 3 kJ/mol, while both OPLS-AA …