Physiologically relevant modeling of biomolecules requires the accurate inclusion of solvation effects. Explicit solvent molecular dynamics provides this but at considerable computational cost. Continuum implicit solvation methods are fast but ignore the discrete, molecular nature of water and require extensive parameterization. In contrast, the 3D-reference interaction site model (3D-RISM) uses statistical mechanics to calculate the equilibrium properties of common explicit-solvent models, including water and co-solvents, around biomolecules of arbitrary shape and size. Here we provide an overview of 3D-RISM and its implementation in the Amber molecular modeling suite. 3D-RISM's capabilities are illustrated using three examples: calculation of the free energy of protein-ligand binding in biotin-avidin complex, the ionic atmosphere around a 24-base pair DNA duplex and the role of hydration in cucurbit[7]uril host-guest system.

Implicit solvent calculations with explicit molecular models in amber with 3D-RISM

244th National Meeting (2012)

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