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GTKDynamo:- Molecular modeling extension for PyMOL

 

GTKDynamo is free/open source software which, together with pDynamo, transforms PyMOL into a powerful interface for molecular modeling. The interface has been designed to facilitate determining reaction pathways in biological systems, specially using hybrid QC/MM (or QM/MM) methods.

Some capabilities include:

  • Pure QC simulations - ab initio and SMO.
  • Pure MM simulations - using AMBER, CHARMM or OPLS force fields.
  • Hybrid QCMM simulations.
  • Single point calculations.
  • Energy minimization.
  • Molecular dynamics.
  • Reaction coordinate scanning.
  • Umbrella sampling.
  • Reaction path calculations - using NEB.

GTKDynamo is available for download for linux and Mac platforms . Please, make sure that you have installed:

  • pDynamo
  • Matplotlib
  • Numpy / Pylab
  • Pymol 1.x
  • pyGTK
  • ORCA, ab initio calculations.

GTKDynamo_overview-page001_800

J. F. R. Bachega, L. F. S. M. Timmers, L. Assirati, L. B. Bachega, M. J. Field, T. Wymore. J. Comput. Chem. 2013, 34, 2190-2196. DOI: http://dx.doi.org/10.1002/jcc.23346

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