Useful Links

General links:

• 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):

• H++

• pcetk: pDynamo's own toolkit for protonation state calculations in proteins.

• PROPKA

• Protein Continuum Electrostatics

• 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.

Biomolecular force fields that pDynamo can use:

• Amber

• CHARMM

• OPLS

Biomolecular simulation programs whose files pDynamo can read:

• Amber

• CHARMM

• Gromacs

• Avogadro: an open source visualization program useful for small molecules.

• EasyHybrid/GTKDynamo: an open source program that interfaces pDynamo and PyMol.

• PyMol: an open source biomolecular visualization program written in Python.

• VMD: an open source biomolecular visualization program.

pDynamo has interfaces to several third party QC programs. These include:

• DFTB+: an open source semi-empirical density functional theory package.

• ORCA: a free package with many options.

• PySCF: an open source package written in Python.

• QCHEM: a commercial package.

• bpython: an interface to the Python interpreter which can help explore, learn and use pDynamo.

• Cython: the language used to interface pDynamo's Python and C code (derived from Pyrex).

• 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.

• PyYAML and YAML: a markup language which is useful for data archiving but is much less verbose than XML.

• SciPy: a series of packages for scientific computing.