(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2005

TUTORIAL 9

Using VMD with AMBER

By Ross Walker

This tutorial is designed to give you an introduction to using VMD with AMBER. How to load AMBER trajectory files, inpcrd files and then how to manipulate the data. It is not designed to exhaustively cover all of the many features that are present in VMD.

Introduction

Visual Molecular Dynamics (VMD http://www.ks.uiuc.edu/Research/vmd/) is a very powerful and feature rich molecular visualisation package for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Its development is funded by the National Institute of Health under the guidance of Klaus Schulten. It is available free of charge to academic researchers and can be downloaded from the above link after registering.

VMD is an ideal tool for visualising results produced by the Sander module of the AMBER software suite. However, its use is not necessarily intuitive. This tutorial is designed therefore to give a brief introduction to visualising and manipulating trajectories produced from AMBER simulations.

This tutorial is based on VMD v1.8.3 (with the updated plugins v1) which at the time of writing (3rd June 2005) was the most up to date version. If you use a different version of VMD you may find that some features are not available or the interface is slightly different. However, it should still be possible to complete the vast majority of this tutorial.

This tutorial also assumes that you are using Linux. If your operating system is different some of the layout and/or procedures may be slightly different.

This tutorial consists of  nine sections:

  1. section1.htm : Loading VMD and Customising the Initial Window Layout

  2. section2.htm : Loading a PDB File

  3. section3.htm : Changing Representations

  4. section4.htm : Loading AMBER inpcrd and restrt files

  5. section5.htm : Aligning Molecules and Measuring RMSD's

  6. section6.htm : Visualising AMBER Trajectories

  7. section7.htm : Saving a Single Set of Coordinates

  8. section8.htm : Following System Parameters Over the Course of a Trajectory

  9. section9.htm : Creating a Movie

CLICK HERE TO GO TO SECTION 1

(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2005