TUTORIAL 1: Using VMD (Duplicate of Amber Workshop Tutorial 9)

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.

TUTORIAL 2: Simulating a small fragment of DNA. (Duplicate of Amber Workshop Tutorial 1)

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 8 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 3: Simulating a solvated protein that contains a non-standard residue. (Duplicate of Amber Workshop Tutorial 4)

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 4: Peptide Folding - Folding TRPCage (Duplicate of Amber Workshop Tutorial 8)

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 experiements. 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.

TUTORIAL 5: Simulating a pharmaceutical compound using antechamber and the Generalized Amber Force Field. (Duplicate of Amber Workshop Tutorial 5)

Antechamber is a set of tools, shipped with AMBER 8, 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: Ligand Binding using MM and QMMM techniques. (Requires AMBER9 for QMMM section)

Antechamber, leap, minimization, md, and targeted md are demonstrated as tools to model a drug bound to the active site of an enzyme. The enzyme and ligand are treated both separately and as a complex. The initial xray structure contains an intermediate of the reaction rather than the full drug molecule. The fragment is used as a target for the actual drug molecule (tazobactam) in a targeted MD simulation of enzyme (beta-lactamase)/ligand complex.

TUTORIAL 7: Thermodynamic Integration

This tutorial shows how to use thermodynamic integration to estimate the free energy of converting toluene to nothing, in water and then compare the results to literature values.

TUTORIAL 8: MMTSB with AMBER

Introduction to using the MMTSB toolset with AMBER.

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