The Molecular Modelling Toolkit (MMTK) is an
open-source
Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized sof ...
software package written in
Python, which performs common tasks in
molecular modelling
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials scie ...
.
, 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
See also
*
Software for molecular mechanics modelling
References
External links
*
Background information
Molecular modelling software
Molecular dynamics software
Python (programming language) software
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