Paper Citing NAMD - Abstract
Malolepsza, Edyta; Straub, John E.
Empirical Maps For The Calculation of Amide I Vibrational Spectra of Proteins From Classical Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7848-7855, JUL 17 2014
New sets of parameters (maps) for calculating amide I vibrational spectra for proteins through a vibrational exciton model are proposed. The maps are calculated as a function of electric field and van der Waals forces on the atoms of peptide bonds, taking into account the full interaction between peptide bonds and the surrounding environment. The maps are designed to be employed using data obtained from standard all-atom molecular simulations without any additional constraints on the system. Six proteins representing a wide range of sizes and secondary structure complexity were chosen as a test set. Spectra calculated for these proteins reproduce experimental data both qualitatively and quantitatively. The proposed maps lead to spectra that capture the weak second peak observed in proteins containing beta-sheets, allowing for clear distinction between alpha-helical and beta-sheet proteins. While the parametrization is specific to the CHARMM force field, the methodology presented can be readily applied to any empirical force field.
