Last Updated 08/22/2013

This online workshop provides an introduction to the AMBER molecular dynamics software and molecular dynamics and visualisation in general. The workshop consists of a series of tutorials from beginner level to advanced. These tutorials are designed to cover running simple minimisations and MD simulations using the sander module of the amber software as well as how to set-up calculations and what to do with non-standard residues. Ideally you should work through these tutorials in the order they appear.

Skip to tutorial listing

Where to get Help and Information

The first question people ask when confronted with a new piece of software is where can I get help? Amber is no different. Amber is a very sophisticated piece of scientific software and as such can appear very daunting to the new user. Fortunately there are a number of places both new and experienced users can go to get help. The best source of help for active users of the Amber software is the amber mailing list and the mailing list archive. Questions sent to this list will go to all active amber uses and so you get the help of the amber community.

Mailing list archive: (all messages posted on the mailing list are stored here).

Mailing list signup information:

For new uses there are, in addition to these tutorials a number of tutorials (of varying quality) available on the amber website:

Other sources of information include the Amber manual (Version 9:, Version 8: as well as the amber website (

Also remember this: GOOGLE is your friend.

You can search the web, the mailing list archive or these tutorials using the following box:

Some Background

"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos. The current version of the code is Amber version 9, which is distributed by TSRI & UCSF subject to a licensing agreement described on the amber website.

A good general overview of the Amber codes can be found in: D.A. Pearlman, D.A. Case, J.W. Caldwell, W.R. Ross, T.E. Cheatham, III, S. DeBolt, D. Ferguson, G. Seibel and P. Kollman. AMBER, a computer program for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to elucidate the structures and energies of molecules. Comp. Phys. Commun. 91, 1-41 (1995).

An overview of the Amber protein force fields, and how they were developed, can be found in: J.W. Ponder and D.A. Case. Force fields for protein simulations. Adv. Prot. Chem. 66, 27-85 (2003). Similar information for nucleic acids is given by T.E. Cheatham, III and M.A. Young. Molecular dynamics simulation of nucleic acids: Successes, limitations and promise. Biopolymers 56, 232-256 (2001).

In this workshop the word amber will refer to the software package which we will be using to run simulations controlled via the Amber force field.

The release consists of about 50 programs, that work reasonably well together. The major programs are as follows:
  • sander: Simulated annealing with NMR-derived energy restraints. This allows for NMR refinement based on NOE-derived distance restraints, torsion angle restraints, and penalty functions based on chemical shifts and NOESY volumes. Sander is also the "main" program used for molecular dynamics simulations, and is also used for replica-exchange, thermodynamic integration, and potential of mean force (PMF) calculations. AMBER 9 also includes all new QM/MM support.
  • pmemd: This is an extensively-modified version (prepared by Bob Duke) of the sander program, limited to periodic, PME simulations. It is faster, and scales better on parallel machines, than sander; hence it is usually the program of choice for "standard", periodic simulations that do not require features it does not support. The AMBER 9 version of pmemd also has support for implicit solvent Generalized Born simulations.
  • nmode: Normal mode analysis program using first and second derivative information, used to find search for local minima, perform vibrational analysis, and search for transition states.
  • LEaP: LEaP is an X-windows-based program that provides for basic model building and Amber coordinate and parameter/topology input file creation. It includes a molecular editor which allows for building residues and manipulating molecules.
  • antechamber: This program suite automates the process of developing force field descriptors for most organic molecules. It starts with structures (usually in PDB format), and generates files that can be read into LEaP for use in molecular modeling. The force field description that is generated is designed to be compatible with the usual Amber force fields for proteins and nucleic acids.
  • ptraj: This is used to analyze MD trajectories, computing a variety of things, like RMS deviation from a reference structure, hydrogen bonding analysis, time-correlation functions, diffusional behavior, and so on.
  • mm_pbsa: This is a script to automate post-processing of MD trajectories, to analyze energetics using continuum solvent ideas. It can be used to break energies energies into "pieces" arising from different residues, and to estimate free energy differences between conformational basins.

In this workshop due to time restraints we will largely concentrate on using the sander module of Amber to run molecular dynamics simulations. For this we will use the following programs from the amber suite: sander, xleap, ptraj and antechamber. For introductions to the other programs available please see the Amber 9 manual and the online tutorials. Note these tutorials were largely designed for Amber 8, they are currently being updated for Amber 9. Most of the tutorials should be equally applicable to either Amber v8 or Amber v9.

Workshop Tutorials

(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.)


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 method1,2 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

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.

If you enjoyed these tutorials and found them useful please consider making a
small donation to help cover my equipment and hosting costs. (Even $1.00 can help)

(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 2006 Movie Sound Bites   Good Alternatives to Google Adsense   The Top 10 Alternatives to Google Adsense   The Amber Mailing List Archive   The Amber Developers Mailing List Archive   What are the alternatives to Google Adsense?   Star Wars Movie Sound Bites   Freely downloadable Movie Sound Bites