Paper Citing NAMD - Abstract
Patel, Dhilon S.; He, Xibing; MacKerell, Alexander D., Jr.
Polarizable Empirical Force Field for Hexopyranose Monosaccharides Based on the Classical Drude Oscillator
JOURNAL OF PHYSICAL CHEMISTRY B, 119:637-652, JAN 22 2015
A polarizable empirical force field based on the classical Drude oscillator is presented for the hexopyranose form of selected monosaccharides. Parameter optimization targeted quantum mechanical (QM) dipole moments, solutewater interaction energies, vibrational frequencies, and conformational energies. Validation of the model was based on experimental data on crystals, densities of aqueous-sugar solutions, diffusion constants of glucose, and rotational preferences of the exocylic hydroxymethyl of d-glucose and d-galactose in aqueous solution as well as additional QM data. Notably, the final model involves a single electrostatic model for all sixteen diastereomers of the monosaccharides, indicating the transferability of the polarizable model. The presented parameters are anticipated to lay the foundation for a comprehensive polarizable force field for saccharides that will be compatible with the polarizable Drude parameters for lipids and proteins, allowing for simulations of glycolipids and glycoproteins.
