This dataset contains simulation data supporting the manuscript: "Free Energy Simulations on a Biomimetic Glucose Receptor: Understanding the Selectivity of GluHUT"by Ryan Eades, Marko Hanzevacki, Adrian J. Mulholland and Anthony P. Davis All simulation data were generated using the AMBER software package. Trajectories are provided in Scripps binpos binary format, along with the corresponding AMBER topology files (compatible with visualization tools such as VMD). The main directory includes the following archived files: UnrestrainedMDₜrajectories. zipRepresentative unrestrained molecular dynamics (MD) trajectories of the empty GluHUT receptor in water, and complexes of GluHUT bound to glucose, galactose, fructopyranose, and fructofuranose. All trajectories are fully solvated and imaged. SMDₜrajectories. zipSteered molecular dynamics (SMD) trajectories for each sugar, where the sugar was dissociated from the GluHUT cavity using time-dependent harmonic restraints. Water molecules were removed from these trajectories to reduce file size. USₜrajectories. zipUmbrella sampling (US) trajectories for each sugar, where the sugar molecule was restrained at specific values of the reaction coordinate using harmonic potentials. Water molecules were removed from these trajectories to reduce file size. WHAMPMF. zipInput and output files from umbrella sampling simulations used for Weighted Histogram Analysis Method (WHAM) calculations to construct the potentials of mean force (PMFs) for each sugar. GIST. zipFully solvated/imaged trajectories of the empty GluHUT receptor, along with input and output files used for Grid Inhomogeneous Solvation Theory (GIST) analysis.
Eades et al. (Wed,) studied this question.