Useful Links
Links to external sites that may prove useful are:
- AMBER File Formats — one of the file formats with which information can be transferred between fDynamo and pDynamo.
- MDL MOL Format — a common molecular file format typically used for representing small molecular systems.
- 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.
- OPLS-AA Force Field — the default force field used by pDynamo.
- 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.
- Pyrex — the language used to interface pDynamo's Python and C code.
- 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.
- Tripos MOL2 Format — a common molecular file format typically used for representing small molecular systems.
- VMD — an open source program for visualizing molecular structures.
