Molecular Modelling Toolkit

Molecular Modelling Toolkit
MMTK
Original author(s) Konrad Hinsen
Initial release 4 January 2000 (2000-01-04)
Stable release 2.7.4 / 28 April 2011; 6 months ago (2011-04-28)
Written in Python, C
Operating system Cross-platform
Type Bioinformatics
Website dirac.cnrs-orleans.fr/MMTK/

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

The Molecular Modeling Toolkit is a library that implements common molecular simulation techniques, with an emphasis on biomolecular simulations. It uses modern software engineering techniques (object-oriented design, a high-level language) in order to overcome limitations associated with the large monolithic simulation programs that are commonly used for biomolecules. Its principal advantages are (1) easy extension and combination with other libraries due to modular library design, (2) a single high-level general-purpose programming language (Python) is used for library implementation as well as for application scripts, (3) use of documented and machine-independent formats for all data files, and (4) interfaces to other simulation and visualization programs.

— Konrad Hinsen, The Molecular Modeling Toolkit: A New Approach to Molecular Simulations, [1]

As of 28 April 2011 (2011 -04-28), MMTK consists of about 18,000 lines of Python code, 12,000 lines of hand-written C code, and some machine-generated C code.

Contents

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

See also

  • Software for molecular mechanics modelling

References

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

External links

_Stub icon 1 Stub icon 2 This bioinformatics-related article is a stub. You can help Wikipedia by expanding it.