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.