Useful Links

Links to external sites that may prove useful are:

    • Biomolecular Force Fields — those that pDynamo can use:
    • AMBER
    • CHARMM
    • OPLS-AA
    • Biomolecular Simulation Programs — those whose files are compatible with pDynamo:
    • AMBER
    • CHARMM
    • 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:
    • MDL MOL Format
      • Tripos MOL2 Format (file taken from old Tripos website)
    • 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:
    • H++
      • pcetk — a pDynamo-based toolkit for protonation state calculations in proteins.
    • PROPKA
    • Protein Continuum Electrostatics
    • 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.