Molecular Modelling Toolkit

The Molecular Modelling Toolkit (MMTK) is an open-source software package written in Python, which performs common tasks in molecular modelling.^[1]

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(As of April 2011), MMTK consists of about 18,000 lines of Python code, 12,000 lines of hand-written C code, and some machine-generated C code.

Features

construction of molecular systems, with special support for proteins and nucleic acids
infinite systems or periodic boundary conditions (orthorhombic elementary cells)
common geometrical operations on coordinates
rigid-body fits
visualization using external PDB and VRML viewers; animation of dynamics trajectories and normal modes
the AMBER 94 force field, with several options for handling electrostatic interactions
a deformation force field for fast normal mode calculations on proteins
energy minimization (steepest descent and conjugate gradient)
molecular dynamics (with optional thermostat, barostat, and distance constraints)
normal mode analysis
trajectory operations
point charge fits
molecular surface calculations
interfaces to other programs

↑ Hinsen K (2000). "The Molecular Modeling Toolkit: A New Approach to Molecular Simulations". J. Comput. Chem. 21 (2): 79–85. doi:10.1002/(SICI)1096-987X(20000130)21:2<79::AID-JCC1>3.0.CO;2-B.

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