4.10. Molecular Dynamics Protocol

The best-scored pose of the selected GAL derivative in complex with AChE was used as a starting structure for the MD simulation by Amber 18 [35]. The small molecule was parametrized using GAFF2.11 force field and AM1-BCC charges, and the complex was solvated in a truncated octahedral box with TIP3P water and 0.15 M NaCl. The system was subjected to energy minimization, heating to 310 K, density equilibration, preproduction equilibration and production dynamics for 1µs (1000 ns). Frames were saved every 1 ns.