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:
- Numpy / Pylab
- Pymol 1.x
- ORCA, ab initio calculations.
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