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ASE interface to the Molecular Modelling Toolkit (MMTK)
The Molecular Modelling Toolkit (MMTK) by Konrad Hinsen is a powerfull program library for molecular simulation.
MMTK's functionality includes construction of molecular systems, including support for proteins and nucleic acids, dynamics, normal mode analysis and much more.
The ASE calculator interface enables the use of ASE dynamics/filters etc, with the MMTK force-fields, in this way the ASE functionality, like the Nudged Elastic Band method and Langevin dynamics, can be added to the MMTK functionality.
For general information on MMTK see the Molecular Modelling Toolkit homepage.
The MMTK ASE calculator can not be attached to a general ListOfAtoms, but must use a ListOfAtom constructed from the MMTK atoms. The reason is that in constructing the force-fields additional information for each atoms must be present; a Carbon atom is not just a Carbon atom. This information is usually supplied in a PDB file.
Setting up the force-field starting from PDB files, the MMTK universe must be handle by MMTK commands.
The examples in the next section shows examples of setting up a MMTK universe.
Once the MMTK universe is constructed a ASE ListOfAtoms can be constructed and attached to a MMTK calculator:
atoms = MMTKListOfAtoms(universe) atoms.SetCalculator(MMTK())
In this example MMTK will be used to add missing Hydrogen for a experimental pdb file.
The example will used the dipeptide.pdb pdb file as an example.
The following MMTK python script will add the missing Hydrogen atoms for the dipeptide:
The added Hydrogen atoms are shown here (orange):