Paper Citing NAMD - Abstract
Nagata, Takeshi; Fedorov, Dmitri G.; Sawada, Toshihiko; Kitaura, Kazuo
Analysis of Solute-Solvent Interactions in the Fragment Molecular Orbital Method Interfaced with Effective Fragment Potentials: Theory and Application to a Solvated Griffithsin-Carbohydrate Complex
JOURNAL OF PHYSICAL CHEMISTRY A, 116:9088-9099, SEP 13 2012
Based on the proposed new expression of the polarization energy for the fragment molecular orbital (FMO) method interfaced with effective fragment potentials (EFPs), we develop an analysis of the solute(FMO)-solvent(EFP) interactions by defining individual fragment contributions for both solute and solvent. The obtained components are compared to all-electron calculations where water is treated as FMO fragments in the pair interaction energy decomposition analysis. The new energy expression is shown to be accurate, and the developed energy analysis is applied to the solvated griffithsin-carbohydrate complex. The details of the ligand recognition are revealed in the context with their interplay with the solvent effects. Tyr residue fragments are shown to reduce the desolvation penalty for Asp, which strongly binds the ligand.
