5 Introductory Case Studies
5.1 Simple Simulation of Alanine Dipeptide
 This tutorial is designed for new users who have little or
no experience with running molecular dynamics simulations. It assumes no
prior knowledge of AMBER or Linux but assumes that AmberTools 20 as well as
XMGRACE are correctly
installed on your system and AMBERHOME is set correctly. If you are new to
AMBER and MD in general this is a good place to start.
By Ben Madej and Ross Walker
5.2 Simulating a DNA polyA-polyT Decamer
 This tutorial
will act as a basic introduction to LEaP, sander and ptraj, to build,
solvate, run molecular dynamics and analyze trajectories. It will also cover
visualising trajectories using
VMD. The aim of this
tutorial is to act as a brief introduction to running classical molecular
dynamics simulations using the AMBER software.
In this tutorial we will create a initial structure for a 10-mer of DNA
and then we will run gas phase, implicit and explicit solvent
simulations on it. Finally we will look at a practical example of how MD
simulations can be used to investigate how A-DNA can convert to B-DNA.
By Ross Walker (based on an original DNA tutorial
developed by Thomas Cheatham)
5.3 Simulating the Green
Fluorescent Protein and building a modified amino acid residue
 In this tutorial, we will learn how to
use the AMBER programs to build a residue template and parameter set for a
custom, modified amino acid. Unlike other tutorials that detail how to
create a residue template and parameter set for a small organic ligand, the
modified amino acid in this example must be bonded to the residues that come
before and after it in the protein polymer sequence. As a result, the
process is more complex and has more steps.
By Jason Swails, Dave Case, and Taisung Lee
5.5 Case Study - Folding TRP
Cage (Advanced analysis and clustering)
 This
tutorial is designed as a case study that will show you how to reproduce the
work discussed in the following paper:
Simmerling, C., Strockbine, B., Roitberg,
A.E., J. Am. Chem. Soc., 2002, 124, 11258-11259
(
http://dx.doi.org/10.1021/ja0273851)
It is a fairly long and in-depth tutorial covering creating structures using
XLeap followed by running heating and long MD simulations to conduct protein
folding experiments. It then moves on to more advanced analysis, including
RMSD fitting, mdcrd to binpos conversion, average structure calculation,
hydrogen bond analysis and dihedral angle tracking using ptraj. We also look
at cluster analysis using the MMTSB toolset. It is recommended that you
complete the Introductory tutorials before
attempting this more advanced tutorial.
By Ross Walker
5.6 Using mdgx to manipulate
small molecules
 A tutorial for people who want to play
with molecules! How does it bend? What shapes can you get it into without
being too aggressive? This tutorial takes a deep dive into the
mdgx engine's conformational sampling module, useful for
generating starting configurations for small peptide simulations, drug
molecule docking, or force field development.
By David Cerutti
| 
This tutorial is a walk-through of one
of Prof Matt Lee's research projects. It will take you through how to set
up, run, and analyze a simulation of the core domain of the HIV-1 integrase
enzyme. (