Difference between revisions of "AMBER TI Tutorials"
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==Introduction to TIMD== | ==Introduction to TIMD== | ||
| − | This is a TIMD tutorial based on the tutorial written by Thomas Steinbrecher on the site[http://ambermd.org/tutorials/advanced/tutorial9/]. But some important changes have been made to suit the current AMBER 10 version according to Miranda's tutorial from Simmerling's lab. | + | This is a TIMD tutorial based on the tutorial written by Thomas Steinbrecher on the site[http://ambermd.org/tutorials/advanced/tutorial9/]. But some important changes have been made to suit the current AMBER 10 version according to Miranda's tutorial from Simmerling's lab[http://simmerlinglab.org/wiki/index.php/Thermodynamic_Integration_%28TI%29_MD]. |
In this tutorial, free energy calculations will be used to calculate the relative binding free energy of two simple ligands, benzene and phenol to the T4-lysozyme mutant L99A. Free energies will be computed by using the thermodynamic integration facilities of the sander program. A modified van-der-Waals equation (softcore potentials) are used to ensure smooth free energy curves. | In this tutorial, free energy calculations will be used to calculate the relative binding free energy of two simple ligands, benzene and phenol to the T4-lysozyme mutant L99A. Free energies will be computed by using the thermodynamic integration facilities of the sander program. A modified van-der-Waals equation (softcore potentials) are used to ensure smooth free energy curves. | ||
Revision as of 15:06, 11 January 2010
Contents
A simple TIMD tutorial about T4-lysozyme
Introduction to TIMD
This is a TIMD tutorial based on the tutorial written by Thomas Steinbrecher on the site[1]. But some important changes have been made to suit the current AMBER 10 version according to Miranda's tutorial from Simmerling's lab[2].
In this tutorial, free energy calculations will be used to calculate the relative binding free energy of two simple ligands, benzene and phenol to the T4-lysozyme mutant L99A. Free energies will be computed by using the thermodynamic integration facilities of the sander program. A modified van-der-Waals equation (softcore potentials) are used to ensure smooth free energy curves.
