Molecular dynamics simulations of α-glucosidase and liquiritigenin

Data source files on RMSD, RMSF,Rg and SASA for molecular dynamics simulations of α-glucosidase(α-Glu) （PDB: 3A4A）at 200ns in the presence or absence of liquiritigenin(LTG).The software used was Gromacs 2023.2.Prior to docking, α-Glu must be de-watered, hydrogenated, and polarised, and the LTG was preprocessed using the Amber force field of the Acpype server to obtain GMX.itp and GMX.gro files for the LTG.

MD simulations were employed using GROMACS software: first, α-Glu and LTG were modeled with Amber99sb and Amber force fields, respectively. Then an ortho-dodecahedral box was built, and solvation and charge neutralization of α-Glu/α-Glu−LTG were performed and energy minimization of the system was carried out using the most rapid descent method. And the system was equilibrated using a canonical ensemble (NVT) and an isothermal-isobaric ensemble (NPT).