Optimize

Type	PyMOL Plugin
Download	plugins/optimize.py
Author(s)	Osvaldo Martin
License	GPL
This code has been put under version control in the project Pymol-script-repo

Introduction

Optimize provides a PyMOL graphical interface to some of the molecular mechanics features available in openbabel, allowing the user to minimize the energy of any molecule uploaded on PyMOL.

Installation

Optimize was tested only on GNU/Linux but should work on other operating systems. The plugin can be downloaded through the project Pymol-script-repo. Optimize needs openbabel to be installed on your computer (see instructions here).

Usage

The plugin can be accessed using a graphic user interface (see figure 0) or from the PyMOL`s terminal trough the following command:

minimize [selection string [, forcefield string [, method string [, nsteps int [, conv float [, cutoff bool [, cut_vdw float [, cut_elec float]]]]]]]

Figure 0: Optimize plugin GUI

Where:

• selection: Select what is going to be minimized. The default value is 'all'. Using the GUI the default value is the first uploaded object.
• forcefield: Select the forcefield used to compute the Internal Energy, options available are GAFF, MMFF94s, MMFF94, UFF and Ghemical.
• method: Select the method used to find the local minimum. The methods available are conjugate gradients and steepest descent.
• nsteps: Number of iteration steps during the minimization.
• conv: Criteria used to judge minimization convergence.
• cutoff: Control if cut-off are used or not to compute non-bonded interactions, posible values are True of False.
• cut_vdw: If cutoff is True, then this parameter set the limit beyond which two atoms do not interact trough Van der Waals forces.
• cut_elec: If cutoff is True, then this parameter set the limit beyond which two atoms do not interact trough electrostatic forces forces.

Change log

• 2013-10-06 (Version 0.1)
  1. First version. (More features coming soon!)
• 2013-10-24 (Version 0.2)
  1. now openbabel add the hydrogen and not PyMOL.

Citation

If you find optimize useful please consider citing this work Noel M. O'Boyle , Michael Banck , Craig A. James , Chris Morley , Tim Vandermeersch and Geoffrey R. Hutchison. "Open Babel: An open chemical toolbox." Journal of Cheminformatics 2011, 3:33. http://www.jcheminf.com/content/3/1/33