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Introduction

These tutorials are prepared by the Amber developers to help you learn how to use the Amber software suite. Please refer to the Amber Reference Manual for syntax and detailed explanations. It is assumed that you are a scientist. Whenever possible, example literature articles are provided. Please do not use these tutorials as protocols but as a starting point to conducting your scientific studies.

Underlined heading titles are linked to a new page of abstracts describing each tutorial.

New Users

For an overview of how to use these tutorials and how to get started with the Amber software suite, please see this overview page.

Amber Tutorials

• 1 Building Systems
  1.1 Preparing Structure
  1.2 Fundamentals of LEaP
  1.3 Building Systems with CHARMM-GUI
  1.4 Hydrogen Mass Repartitioning
  1.5 Building a Peptide Sequence
  1.6 Building Protein Systems in Explicit Water
        • Calculating Salt Molarity in an Explicit Water System
  1.7 Simulation of a protein crystal
  1.8 Un-natural amino acids: the Amber ff15ipq-m force field
  1.9 Building Membrane Systems-Overview
        a. Using PACKMOL-Memgen to Setup and Run a Membrane Simulation
        b. Lipi21 and PACKMOL-Memgen Setup
        c. Lipid-building tutorial using Desmond/Maestro, PyMOL
  1.10 Using the Pantetheine Force Field Library
  1.11 Building and Simulating an Ionic Liquid
  1.12 Material Systems
        a. Protein-Metal
        b. PET polymer
        c. Hydroxyapatite-Water
  1.13 Using 3D-RISM and MOFT to place waters and ions
  

• 2 Developing Nonstandard Parameters
  2.1 Simulating a pharmaceutical compound with Antechamber and GAFF
        • Original antechamber tutorials
  2.2 Setting up a DNA-Ligand System
  2.3 Simulating the Green Fluorescent Protein and building a modified amino acid residue
        • Recent modified-residue tutorial from Carlos Ramos
  2.4 Metal Ion Modeling Tutorial
  2.5 Electrostatic Parameterization with Pyresp.py
  2.6 Deriving Implicitly Polarized Charges with mdgx
  2.7 Deriving Custom Force Field Parameters with mdgx
  2.8 Adding Custom Extra Points to a Model
  

• 3 Creating Stable Systems and Running MD
  3.1 Relaxation of Explicit Water Systems
  3.2 Relaxation of Implicit Solvent System (GB)
  3.3 Running MD with pmemd
  

• 4 Trajectory Analysis
  4.1 An Introduction to CPPTRAJ
  4.2 RMSD Analysis in CPPTRAJ
  4.3 Introduction to Principal Component Analysis with CPPTRAJ
  4.4 Combined Clustering Analysis with CPPTRAJ
  4.5 AMBER-Hub CPPTRAJ website
  4.6 Analysis of MAD2 using PCA, tICA, and Markov State Models
  

• 5 Case Studies
  5.1 Simple Simulation of Alanine Dipeptide
  5.2 Simulating the Green Fluorescent Protein and building a modified amino acid residue
        • Simulating the MTR1 ribozyme, from the York group
  5.3 Using mdgx to manipulate small molecules
  5.4 Calculating ion distributions around DNA using 3D-RISM
  

• 6 Sampling Configuration Space
  6.1 Adaptive Steered Molecular Dynamics
  6.2 The unified “middle” thermostat scheme for efficient configurational sampling
  6.2 Weighted Ensemble Methods using WESTPA
  

• 7 Free Energies
  7.1 Thermodynamic Integration using soft core potentials
  7.2 Advanced Thermodynamic Integration Using ACES
  7.3 pKa Calculations using Thermodynamic Integration
  7.4 Molecular Mechanics with a Poisson‐Boltzmann/Surface Area solvent: MM-PBSA
  7.5 Umbrella sampling: A Potential of Mean Force in alanine dipeptide Phi/Psi rotation
  7.6 Umbrella sampling: Transferring methanol through a membrane
  7.7 Free energy estimation for conformers of dialanine using EMIL
  7.8 Computing binding enthalpy values
  7.9 Free energy calculations with the Free Energy Workflow Tool (FEW)
  7.10 Grid Inhomogeneous Solvation Theory for water thermodynamics: in Factor Xa
  7.11 Computing Binding Free Energy using the Attach-Pull-Release (APR) Method
        • More recent tutorial from the Gilson group
  7.12 The Nonequilibrium Free Energy (NFE) Toolkit for pmemd
  

• 8 Chemical Reactions and Equilibria
  8.1 Constant pH MD example: Calculating pK_as for titratable side chains in Lysozyme
  8.2 Constant pH and Redox Potential MD example: predicting pH-dependent E^o values
        • Example of computing Marcus electron transfer parameters, using Amber plus other tools
  8.3 Quantum dynamical effects in liquid water: diffusion and IR spectra
  

• 9 Tools
  

Deprecated Tutorials

This is a list of deprecated tutorials. These may have used older versions of Amber or methods that are no longer commonly employed. Some tutorials are deprecated because there are newer versions in process and/or too many updates are required to make the current version useful for new users. As new tutorials are made, they will be populated above and current ones deprecated.

Japanese Versions

• by Akira Wadano and Takenori Kanai
• by Conflex corporation