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:
How to cite:
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