Molecular Modelling Toolkit
The Molecular Modelling Toolkit (MMTK) is an open-source software package written in Python, which performs common tasks in molecular modelling.
As of 28 April 2011[update], 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