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. Pymol has been chosen as a graphical interface to pDynamo because it has a python API with wide documentation available. The code has been written by José Fernando R. Bachega, under advertisement of prof. Richard Charles Garratt and Dr. Troy Wymore, and a tremendous contribution from Dr. Martin Field.

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.
  • and more...

How to cite:

GTKDynamo paper

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: 10.1002/jcc.23346