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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

dna 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

GFP Beta Barrel 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

5.4 Loop dynamics of the HIV-1 integrase core domain

HIV-1 integrase core domain 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. (Japanese translation)

By Matt Lee

5.5 Case Study - Folding TRP Cage (Advanced analysis and clustering)

TRP cage 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 (
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

vmd 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

"How's that for maxed out?"

Last modified: Mar 24, 2021