The recently updated AMBER tools now includes software to analyse the structure and thermodynamics of water at protein and other surfaces. In addition to 3D-RISM, AMBER Tools now includes a new method, called Grid Inhomogeneous Solvation Theory, uses the same underlying theory as WaterMap but generates 3D grids of water properties, rather than focusing on discrete hydration sites.
The method is described in this paper, Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbituril DOI.
Solvation and desolvation plays a critical role in ligand binding but can be difficult to determine computationally.
AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. AmberTools is distributed in source code format, and must be compiled in order to be used. You will need C, C++ and Fortran90 compilers.