MOLE: a website for locating and characterizing channels, pores and tunnels in proteins.
Packmol: a useful program for preparing condensed phase systems for simulation; e.g. solvated macromolecules.
Protein Data Bank: the definitive source for experimentally-determined biomacromolecular structures.
pKa determination (mostly for proteins):
Molecular File Formats
MDL MOL Format: a commonly used format for small molecules.
Open Babel: a very useful open source program for converting different molecular representations and other miscellaneous tasks.
SMILES: a string-based notation for specifying the composition and covalent bond pattern of a molecular system.
Tripos MOL2 Format: another commonly used format for small molecules.
bpython: an interface to the Python interpreter which can help explore, learn and use pDynamo.
iPython: another interface to the Python interpreter which can help explore, learn and use pDynamo.
NumPy: a package for numerical computing in Python.
Python: the language in which most of pDynamo is written.
SciPy: a series of packages for scientific computing.