BEGINNER'S CORNER: Learning the Unix Command-line

A computer is like any other scientific instrument in that you need to have a basic understanding of how it works and, more importantly, how to use it to do your work, before you can hope to to carry out meaningful calculations with any computational chemistry package, including AMBER.

Without a basic knowledge of how to navigate a filesystem, execute commands, or create and modify files and folders, you will be unlikely to understand what is being done in these tutorials well enough to learn AMBER. Most of these tutorials assume a decent level of experience and competency with Unix command-line use, and as such expect that basic concepts of using the command-line and common commands are part of a standard vocabulary. You should develop this vocabulary so that trying to learn the command-line while performing the tutorials does not replace trying to learn how to use AMBER itself.

The link provided at the top navigates to an interactive Unix tutorial through Code academy, and is sufficient for beginners. You will need to create a free login to use it. This is by no means the only resource available for learning Unix, but it seems to be fairly thorough.

By codecademy; No affiliation with AMBER

LEaP Tutorial

This tutorial is written for beginners of LEaP, which is the main program for preparing the topology and coordinate files for AMBER. The tutorial gives comparison of different kind of files used in the LEaP program, introduces the workflow of LEaP for doing modeling. In the end a quick example of a protein-ligand complex was shown.

By Pengfei Li

TUTORIAL B0: An Introduction to Molecular Dynamics Simulations with AMBER

This tutorial is designed for new users who have little or no experience with running molecular dynamics simulations. It assumes no prior knowledge of AMBER or Linux but assumes that AmberTools 14 as well as VMD are correctly installed on your system and AMBERHOME is set correctly. If you are new to AMBER and MD in general this is the place to start.

By Ben Madej & Ross Walker

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

TUTORIAL B3: Case Study - Folding TRP Cage (Advanced analysis and clustering)

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

TUTORIAL A8: Loop dynamics of the HIV-1 integrase core domain

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. (Japanese translation)

By Matt Lee

TUTORIAL B4: Simulating a pharmaceutical compound using antechamber and the Generalized Amber Force Field.

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. (Ukranian translation; Japanese translation)

By Ross Walker and Sishi Tang

TUTORIAL B5: Simulating the Green Fluorescent Protein and building a modified amino acid residue

In this tutorial, we will learn how to use the AMBER programs to build a residue template and parameter set for a custom, modified amino acid. Unlike other tutorials that detail how to create a residue template and parameter set for a small organic ligand, the modified amino acid in this example must be bonded to the residues that come before and after it in the protein polymer sequence. As a result, the process is more complex and has more steps.

By Jason Swails, Dave Case, and Taisung Lee

Tutorial A1: Setting up a DNA-Ligand System

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

TUTORIAL A1 Old: Building your own Custom Residues (old version)

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
 

TUTORIAL A20: Metal Ion Modeling Tutorial

In this tutorial we will delineate several modeling strategies of metal ions in mixed systems (proteins and nucleic acids) using the AmberTools package. Both the bonded model and nonbonded model are illustrated. For the bonded model, MCPB and MCPB.py are used to facilitate the modeling. While for the nonbonded model modeling strategies for the 12-6 Lennard-Jones (LJ) and 12-6-4 LJ-type nonbonded models are presented. (Japanese translation)

By Pengfei Li & Kenneth M. Merz Jr.

TUTORIAL A2: A simple coupled potential QM/MM/MD simulation.

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 came the ability to do very fast advanced coupled potential QM/MM driven minimization and MD. This tutorial will show you how to set up a simple QM/MM/MD simulation of NMA in solution.

By Ross Walker

TUTORIAL A23: Generating Force Field Parameters with Paramfit

In this tutorial we will generate force field parameters for two small moleculesfrom ab-initio quantum calculations using the AmberTools program Paramfit. This tutorial generates the phi and psi dihedral potentials over two different small peptide chains, and details each step of the parameter generation process from preparation of a conformational sampling of each structure to generation of quantum data to evaluating the quality of the resulting parameters.

By Robin M. Betz

TUTORIAL A16: An Amber Lipid Force Field Tutorial: Lipid14

Updated for Lipid14
Phospholipid bilayers are essential components to cellular membranes and are the stage where many essential biophysical and biochemical processes take place. This tutorial explains how to set up and simulate lipid bilayers with the Lipid14 force field. A DOPC bilayer is built, converted, and loaded into LEaP to assign parameters for molecular dynamics simulation. A molecular dynamics scheme is presented followed by analysis of the bilayer structural properties in the trajectory. Furthermore, membrane-bound proteins are examined and a simple membrane-bound protein system is built.

By Ben Madej & Ross Walker

Parker de Waal has created an alternative lipid-building tutorial using Maestro.

TUTORIAL A15: Simulations of a room-temperature ionic liquid

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

TUTORIAL A27: Material Systems Modeling Tutorial

Together with the INTERFACE force field, this tutorial explores the functions of employing the AMBER software package to modeling material and interfacial systems.

By Pengfei Li

TUTORIAL C0: An Introduction to CPPTRAJ

This tutorial will give a basic introduction to using CPPTRAJ for performing trajectory analysis. It will cover using CPPTRAJ interactively and in batch mode for processing scripts, loading topologies and trajectories, processing data, and working with data sets. (Japanese translation)

By Daniel R. Roe

TUTORIAL C1: RMSD Analysis in CPPTRAJ

This tutorial will give a basic introduction to performing RMSD calculations with CPPTRAJ. It will cover loading reference structures, as well as calculating RMSD to references with different topologies. (Japanese translation)

By Daniel R. Roe

TUTORAL C2: Analysis of Nucleic Acid Simulations

This tutorial will go over using CPPTRAJ to analyze data from simulation of a nucleic acid system.

By Thomas E. Cheatham III, Christina Bergonzo & Rodrigo Galindo-Murillo

TUTORAL C3: Introduction to Principal Component Analysis with CPPTRAJ

This tutorial will go over using CPPTRAJ to perform principal component analysis in Cartesian space.

By Thomas E. Cheatham III, Daniel R. Roe & Rodrigo Galindo-Murillo

TUTORAL C4: Combined Clustering Analysis with CPPTRAJ

This tutorial will cover how to perform combined clustering analysis with CPPTRAJ, which is a way of comparing structure populations between two or more independent trajectories or between different parts of a single trajectory.

By Daniel R. Roe

TUTORAL C5: Hydrogen Bond Analysis with CPPTRAJ

This tutorial will cover how to perform hydrogen bond analysis with CPPTRAJ.

By Daniel R. Roe

TUTORIAL P0: An Introduction to PYTRAJ

This tutorial will give a basic introduction to using PYTRAJ for performing trajectory analysis in Jupyter notebook.

By Hai Nguyen

TUTORIAL P1: Simulating Crystals with the AMBER Molecular Dynamics - Jupyter notebook version

This tutorial combines Jupyter notebok, pytraj and protein viewer and other packages in AMBER for seting up system for crystal simulation.

By Hai Nguyen

TUTORIAL P2: Using Jupyter notebook remotely

This tutorial will guide you how to use Jupyter notebook remotely.

By Hai Nguyen

TUTORIAL P3: Using NGLView for protein visualization in Jupyter notebook

This tutorial will guide you how to use NGLView to visualize MD trajectories in Jupyter notebook and to use pytraj to perform data analysis.

By Hai Nguyen

TUTORIAL P4: Trajectory rendering and movie making with NGLView

This tutorial will guide you how to use NGLView to visualize MD trajectories in Jupyter notebook and to quickly make a movie for presentation.

By Hai Nguyen

TUTORIAL P5: Real time molecular dynamics simulation and visualization

This tutorial will guide you how to use AmberTools and NGLView to perform molecular dynamics simulation and visualize the trajectory in real time.

By Hai Nguyen

TUTORIAL A3: MM-PBSA

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 to perform these calculations as well. (Japanese translation)

By Ross Walker & Thomas Steinbrecher

TUTORIAL A24: Free energy calculations with the Free Energy Workflow Tool (FEW)

This tutorial demonstrates the functionality of the Free Energy Workflow tool FEW. Using a sample data set of inhibitors of the protein Factor Xa it is shown how FEW can be used to easily prepare MD simulations and binding free energy calculations by the MM-PB(GB)SA, the linear interaction energy (LIE), and the thermodynamic integration (TI) method for multiple ligands binding to the same receptor. FEW provides an efficient way to setup and conduct binding free energy calculations with AMBER.

By Nadine Homeyer & Holger Gohlke

TUTORIAL A7: Replica Exchange

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

TUTORIAL A12: Conformational equilibria of poly-proline pentamer

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

TUTORIAL A22: Using Accelerated Molecular Dynamics (aMD) to enhance sampling

In this tutorial, we will learn how to use AMBERs implementation of aMD to enhance sampling. In this tutorial we focus on the steps necesary to prepare and run an aMD simulation. We use the work we published on the discovery of long lived conformational transformations in the Bovine Pancreatic Trypsin Inhibitor (BPTI) protein. We follow the preparation of the files and give sme information about amd reweighting.

By Romelia Salomon Ferrer , Levi Pierce & Ross Walker

TUTORIAL A10: Steered molecular dynamics of a proton transfer reaction

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

TUTORIAL A26: Adaptive Steered Molecular Dynamics

This tutorial provides detailed instructions on how to perform Adaptive Steered Molecular Dynamics Simulations (ASMD). Compared to Steered Molecular Dynamics, ASMD has been shown to converge much faster while reducing the computational cost. The tutorial calculates the Potential Mean Force of unfolding a small alpha-helical peptide using two different velocities.

By T. Dwight McGee Jr., Hailey Bureau, Caley Allen & Rigoberto Hernandez

TUTORIAL A11: Conformational equilibria of methyl-alpha-L-iduronic acid in explicit water

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

TUTORIAL A5: Nudged Elastic Band [AMBER v11 or later only]

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

TUTORIAL A18: Constant pH Molecular Dynamics Example - Calculating pK_as for titratable side chains in HEWL

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.

TUTORIAL A6: pKa Calculations using Thermodynamic Integration [AMBER v9 and later]

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

TUTORIAL A17: Umbrella Sampling Example - Calculating the PMF for Alanine Dipeptide Phi/Psi Rotation

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

TUTORIAL A9: Thermodynamic Integration using soft core potentials

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

TUTORIAL A19: Free Energy Estimation for Conformers of Dialanine using EMIL [AMBER v14 and later]

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

TUTORIAL A21: Computing Binding Enthalpy Values

In this tutorial, we will learn how to use AMBER to compute precise binding enthalpies using explicit water molecular dynamics simulations. Here we focus on the guest B2 binding to the host CB7. However, while the example in this tutorial focuses on a host-guest system, the technique is directly applicable to protein-ligand systems although we caution that the such systems will require considerably more sampling to converge than the host-guest system in this tutorial.

By Andrew T. Fenley & Michael K. Gilson

TUTORIAL A4: NMR Refinement of DNA and RNA Duplexes

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

TUTORIAL A13: Simulation of a protein crystal

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

TUTORIAL A14: Using 3D-RISM to place waters

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

TUTORIAL A25: Analysis of water thermodynamics using Grid Inhomogeneous Solvation Theory of Factor Xa active site

In this tutorial we will learn how to use the AMBER software coupled with the Grid Inhomogeneous Solvation Theory Method (GIST) to estimate thermodynamic values for the water molecules occupying the binding pocket of Factor Xa. Often one might want to estimate changes in hydration which are central to correctly describe biomolecular phenomena such as molecular recognition, drug binding, etc. However it is difficult to estimate precisely the thermodynamic solvation contribution in these phenomena.

By Romelia Salomon, Crystal Nguyen, Steven Ramsey, Jonathan D. Gough & Ross Walker