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OS: Linux, Windows, Mac, ...

License: Freeware

The Molecular Modelling Toolkit (MMTK) is an Open Source program library for molecular simulation applications. In addition to providing ready-to-use implementations of standard algorithms, MMTK serves as a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular simulations.

The three most common usage patterns of MMTK are

Writing Python scripts that make use of MMTK functions for standard simulation and modelling applications. This is similar to using other simulation packages with a scripting language (i.e. CHARMM or Gromos), but with the added advantage of having access to lots of useful Python modules from elsewhere. The example section shows what such scripts look like.
Writing modules that interact closely with MMTK (and perhaps other packages) to solve problems for which no standard solution exists. For example, adding a particular force field term or a particular simulation or analysis algorithm. There is not much competition for MMTK in that domain.
Writing application programs in Python that use MMTK internally, for users that do not need to know anything about such internals. Those programs can provide easy-to-use graphical interfaces (see e.g. DomainFinder and nMOLDYN) or be integrated into a Web service (see e.g. WEBnm@).

MMTK's functionality includes

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