Amber Tutorials

TUTORIAL B1: Simulating a small fragment of 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)

TUTORIAL B2: Using VMD with AMBER

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.

By Ross Walker

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 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 earlier tutorials in this listing before attempting this more advanced tutorial.

By Ross Walker
 

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). Then we set up a simulation of sustiva bound to HIV-RT. (Ukrainian translation)

By Ross Walker and Sishi Tang
 

This tutorial covers setting up an advanced system. In this case it shows you how to set up a dye system that is covalently bound to DNA. It also includes manually running multiconformational RESP fits, building custom units and assigning parameters manually.

By Bryan Leland, David Paul, Brent Krueger and Ross Walker
 

This tutorial is somewhat replaced by tutorial A1 above, however, it is kept here since it does show a useful example of how to create a system containing a metal atom.

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 B4).  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.

By Ross Walker
 

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.

By Ross Walker
 

This tutorial provides a step by step explanation of using the mm_pbsa script to calculate the binding energy of the RAS-RAF protein complex. It also includes instructions on using the mmpbsa_py script (in Amber11) to perform these calculations as well.

By Ross Walker & Thomas Steinbrecher
 

This tutorial provides a basic introduction to using AMBER for NMR refinement of a DNA duplex. It makes use of LEaP and Sander.

[Related information: Mike Summers has prepared a set of scripts for RNA refinement. It contains descriptions, examples, and scripts that were used to generate initial structures with cyana and refined with Amber. Nearly all steps (file conversions, etc.) are written into scripts so that the process can be followed. Some scripts may need tweaking, depending on your operating system. The work is described in: J. Biomol. NMR 47, 205-219 (2010).]

By Vickie Tsui & Rhonda Torres
 

This tutorial uses a feature that is only available with Amber v11. As such you need to have Amber 11 installed to run the calculations in this tutorial, if you are using Amber 9 or 10 then you should use the older NEB tutorial. In the nudged elastic band method, 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.

By Christina Bergonzo, Carlos Simmerling & Ross Walker

This tutorial reproduces the calculation of the pKa value of the ASP residue in the protein thioredoxin as described in the following paper:

Simonson, T., Carlsson, J., Case, D.A., "Proton Binding to Proteins: pKa Calculations with Explicit and Implicit Solvent Models", JACS 2004, 126, pp4167-4180.

By Ross Walker & Mike Crowley
 

This tutorial covers how to setup, run and postprocess replica exchange simulations using multisander and Amber 10 or later.

By Dan Roe, Asim Okur, Carlos Simmerling and Ross Walker
 

This tutorial is a walk-through of one of Prof Matt Lee's research projects.

It will take you through how to setup, run and analyze a simulation of the core domain of the HIV-1 integrase enzyme.

By Matt Lee
 

This tutorial computes the relative binding free energy of two ligands bound to a lysozyme mutant. In three steps, you will learn about the background of soft core TI calculation, the new system setup for Amber10 or later, and how to run and analyze a short free energy calculation.

By Thomas Steinbrecher
 

This tutorial illustrates the use of steered molecular dynamics and a QM/MM energy to compute the barrier to proton transfer in malonaldehyde.

By M.L. Dodson and V. Babin
 

This tutorial illustrates the use of conformational "flooding" to setup a Hamiltonian replica exchange simulation of a small molecule in explicit solvent.

By V. Babin and C. Sagui
 

This tutorial describes a couple of ways to assess conformational equilibria of a short polyproline peptide using so called steered molecular dynamics, and the famous replica-exchange protocol: html, pdf, polyproline-tutorial-files.tar.bz2 (Warning: 60Mb).

By V. Babin and C. Sagui
 

This tutorial describes one way to set up a simulation of a protein crystal, showing how to construct unit cells, and how to fill in missing solvent.

By Dave Cerutti
 

This tutorial shows how the 3D-RISM method can be used to generate an initial configuration of water around a solute molecule.

By Daniel Sindhikara
 

This tutorial illustrates the use of antechamber and sander to carry out some simple simulations of a room-temperature (non-biological!) ionic liquid.

By Chris Lim
 

Phospholipid bilayers are the stage where many essential biophysical and biochemical processes take place. Between the intracellular and extracellular environments, the lipid bilayer itself is an important component. This tutorial explains how to set up and simulate some simple lipid bilayers with the Lipid11 force field. A DOPC bilayer is built, converted, and loaded into LEaP to assemble the parameters for molecular dynamics simulation. A simple minimization, heating, and production scheme is presented followed by a simple analysis of the trajectory. Furthermore, membrane-bound proteins are examined and a simple membrane-bound protein system is built.

By Ben Madej & Ross Walker
 

In this tutorial we will learn how to use the AMBER software coupled with the Weighted Histogram Analysis Method (WHAM) of Alan Grossfield to generate potentials of mean force. Often one might want to know what the free energy profile is along a specific reaction coordinate. Such a profile is known as a potential of mean force and it can be very useful for identifying transition states, intermediates as well as the relative stabilities of the end points. At first thought one might think that you could generate a free energy along a specific reaction coordinate by just running an MD simulation and then looking at the probabilities of the states sampled. However, often the energy barrier of interest is many times the size of k_bT and so the MD simulation will either remain in the local minimum it started in or cross to different minima but very very rarely sample the transition state. Umbrella sampling offers a way to effectively force the system to move through a transition state and reaction pathway that chemical knowledge of the system under study suggests is important.

By Ross Walker & Thomas Steinbrecher
 

In this tutorial we will learn how to use the AMBER software to perform molecular dynamics simulations at constant pH (CpHMD). Solution pH affects titratable side chains in proteins (and, on occasion, ribozymes), which can have a dramatic impact on the function, structure, and stability of large biomolecules. CpHMD is a method that uses a hybrid molecular dynamics/Monte Carlo approach to sample conformations and protonation states of various titratable residues in biomolecules. This method can help capture the coupling between protein structure and pH.

By Jason Swails & T. Dwight McGee Jr.
 

This tutorial is a walk-through of absolute free energy calculations using EMIL. EMIL works by perturbing the "normal" atomistic representation of the system into a model for which the free energy is exactly known, thus it is a sort of thermodynamic integration tool. The example in this tutorial is an estimate of the four free energy basins of the alanine dipeptide.

By Joshua T. Berryman