Difference between revisions of "AMBER TI Tutorials"

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==Generate Start Structures==
==Generate Start Structures==
==Setup MD==
==Post-process/Analyze the data==

Revision as of 16:08, 11 January 2010

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.

Thermodynamic cycle and Method

Setup System

Generate Start Structures

Setup MD

Post-process/Analyze the data