SSTMap implements two approaches for mapping water structure and thermodynamics on to solute surfaces, such as protein binding sites, the hydration site analysis (HSA) and Grid Inhomogeneous Solvation Theory (GIST). The command lines to run each of these analyses are simply
run_gist which are the main command-line tools in
SSTMap. Here we provide examples of the command line arguments required to run these analyses with different popular MD packages.