Difference between revisions of "AMBER TI Tutorials"
From Rizzo_Lab
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==Thermodynamic cycle and Method== | ==Thermodynamic cycle and Method== | ||
| − | ==Setup System== | + | |
| + | ==Setup of the T4 System== | ||
==Generate Start Structures== | ==Generate Start Structures== | ||
| − | ==Setup MD== | + | ==Setup and run MD== |
| − | ==Post-process | + | ==Post-process== |
Revision as of 15:08, 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.
