TUTORIAL 1: Simulating a small fragment of DNA. (Beginner)

This tutorial will act as a basic introduction to LEaP, sander and ptraj, to build, solvate, run molecular dynamics and analyse trajectories. It will also cover visualising trajectories using VMD. This tutorial is an adaptation of the main DNA tutorial provided with the AMBER software. It's aim is to act as a brief introduction to running classical molecular dynamics simulations using the AMBER software. If you are already familiar with AMBER and/or have already completed the online DNA tutorial then you can skip this and move straight on to tutorial 2.

TUTORIAL 2: Using dynamics simulations to estimate binding energetics. (Beginner)

The purpose of this tutorial is to begin thinking about how one might estimate energetics of binding. Here we will obtain some estimated binding energies for a protein ligand system using a short MD simulation. In this tutorial you will be expected to setup the calculation yourself using your experience from tutorial 1 and as such the notes will be much briefer.

TUTORIAL 3: Examining the pKa's of Asp and Glu residues. (Beginner)

The aim of this tutorial is to show how one can use Amber's GB model and minimisation routines to estimate the pKa shifts for glutamic acid and aspartic acid residues in proteins. We will examine two different structures from an NMR ensemble and calculate the pKa shift in each case. The results should show that the shift in pKa is very much dependent on the protein conformation.

TUTORIAL 4: Simulating a solvated protein that contains a non-standard residue. (Intermediate)

Often you will want to simulate a protein system that contains a non-standard residue such as a co-enzyme or an inhibitor. In this case you cannot simply build the topology and coordinate files. You first need to generate a new unit in xleap, add any missing parameters and charges and then create your prmtop and inpcrd files. If the non-standard residue is a standalone molecule then you could use Antechamber for this (see tutorial 5).  However, in this this tutorial we will model plastocyanin which has a copper atom bound to four close residues. This tutorial will give an example of how to build this residue unit in xleap.
There are two versions of this tutorial. A simple version which creates just a new copper residue and approximates it as a +1 ion and a more advanced version where new special histidine and methionine residues are created so that different charges and bond / angle and dihedral parameters can be used.

TUTORIAL 5: Simulating a pharmaceutical compound using antechamber and the Generalized Amber Force Field. (Intermediate)

Antechamber is a set of tools, shipped with AMBER, that can be used to prepare "prep" input files for organic molecules, which can then be read into LEaP and used to create prmtop and inpcrd files. The Antechamber suite is designed for use with the "general AMBER force field (GAFF)" and is ideal for setting up simulations involving organic pharmaceutical compounds or other organic molecules. In this tutorial we will use antechamber to create a leap input file for BMS's HIV reverse transcriptase inhibitor  sustiva (efavirenz).

TUTORIAL 6: A simple coupled potential QM/MM/MD simulation. (Intermediate)

(Updated for AMBER 9): The tutorials up to this point have all used the classical amber force field equation to minimise the system and propagate the dynamics. With the release of AMBER 9 comes the ability to do very fast advanced coupled potential QM/MM driven minimisation and MD. This tutorial will show how to set up a simple QM/MM/MD simulation of NMA in solution using AMBER 9. Although AMBER 8 is no longer recommended for running QM/MM MD simulations An AMBER 8 version of this tutorial is available here.

TUTORIAL 7: Nudged Elastic Band [AMBER v9 only] (Advanced)

This tutorial uses a feature that is only available with Amber v9. As such you need to have Amber 9 installed to run the calculations in this tutorial. In the nudged elastic band method^1,2 the path for a conformational change is approximated with a series of images of the molecule describing the path. Minimisation of the entire system, but with the end point structures fixed, provides a minimum energy path. In this tutorial we will use the NEB method to predict a pathway for a conformational change in alanine dipeptide.

TUTORIAL 8: Case Study - Folding TRP Cage (Advanced)

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 advanced results analysis including advanced RMSd fitting, mdcrd to binpos conversion, average structure calculation, hydrogen bond analysis and dihedral angle tracking using ptraj. As well as cluster analysis using the MMTSB toolset. It is recommended that you complete the earlier tutorials in this listing before attempting this more advanced tutorial. This tutorial has been updated to cover both AMBER 8 and AMBER 9.

TUTORIAL 9: Using VMD with AMBER (Intermediate)

This tutorial acts as a brief introduction to using VMD for visualising AMBER inpcrd, restrt and trajectory files. While only scratching the surface of what VMD can do it covers setting up a .vmdrc file to set the default layout of VMD, loading static structures and performing RMSD fits between similar structures. It then goes on to cover loading and visualising AMBER trajectories, both from gas phase/implicit solvent simulations and from periodic boundary simulations and shows how to save individual frames from a trajectory as well as create an MPEG video of the trajectory.

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