Python and other resources
Practical Computational Chemistry
MD tools
Arpeggio: Webserver for calculating interatomic interactions in protein structures.
PLIP: Protein-Ligand Interaction Profiler (PLIP).
Waterdock: Tool that predicts the location of water molecules in protein structures.
Autodock: Suite of automated docking tools
MDAnalysis: Python library to analyze trajectories from molecular dynamics simulations.
VMD: Molecular visualization program for displaying, animating, and analyzing MD trajectories and pdbs.
Chimera: Molecular visualization program for displaying coordinates (pdbs, mol2, etc) and density maps.