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Useful Links

Links to external sites that may prove useful are:

  • Biomolecular Force Fields — those that pDynamo can use:
  • Biomolecular Simulation Programs — those whose files are compatible with pDynamo:
  • Cython — the language used to interface pDynamo's Python and C code (derived from Pyrex).
  • GTKDynamo — an interface between pDynamo and PyMol.
  • Molecular File Formats:
  • MOLE — a website for locating and characterizing channels, pores and tunnels in proteins.
  • Open Babel — a very useful open source program for interconverting different molecular representations.
  • ORCA Quantum Chemistry Program — an ab initio and DFT quantum chemistry program that can be used in conjunction with pDynamo.
  • pKa Determination — mostly for proteins:
  • Protein Data Bank — a data base of experimentally-determined macromolecular structures.—
  • PyMol — an open source program for visualizing molecular structures.
  • PyYAML and YAML — a markup language which is useful for data archiving but is much less verbose than XML.
  • Python — the language in which most of pDynamo is written.
  • SMILES — a string-based notation for specifying the composition and covalent bond pattern of a molecular system.
  • VMD — an open source program for visualizing molecular structures.