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Amber Tutorials

Below are tutorials prepared by the Amber developers to help you learn how to use the Amber software suite. We encourage users to refer to the Amber Reference Manual for syntax and detailed explanations. As well, we assume you are a scientist and read the appropriate literature. Whenever possible, example literature articles are provided. Please do not use these tutorials as protocols.

Overview: For an overview of how to use these tutorials and where to start, please see this page.

*There are also two sets of Japanese versions: one from Akira Wadano and Takenori Kanai, and a second prepared by Conflex corporation.

• 1 Building Systems
  1.1 Using pdb4amber
  1.2 Fundamentals of LEaP
  1.3 Hydrogen Mass Repartitioning
  Building Specific Types of Systems
  1.4 Building a Peptide Sequence
  1.5 Building Protein Systems in Explicit Water
      •1.5b Calculating Salt Molarity in an Explicit Water System
  1.6 Simulation of a protein crystal
  1.7 The AMBER ff15ipq-m Force Field Tutorial
  1.8 Building Membrane Systems-Overview
      •1.8a Using PACKMOL-Memgen to Setup and Run a Membrane Simulation
      •1.8b Building Systems with CHARMM-GUI
      •1.8c An Amber Lipid Force Field Tutorial: Lipid14
  1.9 Building and Simulating an Ionic Liquid
  1.10 Material Systems
        • Protein-Metal
        • PET Polymer
        • Hydroxyapatite-Water
  1.11 Using 3D-RISM and MOFT to place waters and ions
  

• 2 Developing Nonstandard Parameters
  2.1 Simulating a pharmaceutical compound using Antechamber and the Generalized Amber Force Field
  2.1b 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
  2.4 Metal Ion Modeling Tutorial
  2.5 Deriving Implicitly Polarized Charges in mdgx
  2.6 Deriving Custom Force Field Parameters with mdgx
  2.7 Adding Custom Extra Points to a Model
  2.8 Building your own Custom Residues (old version)
  2.9 [Deprecated] Generating Force Field Parameters with Paramfit
  

• 3a Creating Stable Systems Through Relaxation
  3.1 Relaxation of Explicit Water Systems
  3.2 Relaxation of Implicit Solvent System (GB)
  

• 3b Running MD
  3.3 Running MD with pmemd
  

• 4 Trajectory Analysis
  4.1 An Introduction to CPPTRAJ
  4.2 RMSD Analysis in CPPTRAJ
  4.3 Analysis of a nucleic acid simulation
  4.4 Introduction to Principal Component Analysis with CPPTRAJ
  4.6 Combined Clustering Analysis with CPPTRAJ
  4.6 Hydrogen Bond Analysis with CPPTRAJ
  

• 5 Introductory Case Studies
  5.1 Simple Simulation of Alanine Dipeptide
  5.2 Simulating a DNA polyA-polyT Decamer
  5.3 Simulating the Green Fluorescent Protein and building a modified amino acid residue
  5.4 Loop dynamics of the HIV-1 integrase core domain
  5.5 Case Study - Folding TRP Cage (Advanced analysis and clustering)
  5.6 Using mdgx to manipulate small molecules
  

• 6 Sampling Configuration Space
  6.1 Replica Exchange
  6.2 Conformational equilibria of poly-proline pentamer
  6.3 Using Accelerated Molecular Dynamics (aMD) to enhance sampling
  6.4 Adaptive Steered Molecular Dynamics
  6.5 Conformational equilibria of methyl-alpha-L-iduronic acid in explicit water
  6.6 Nudged Elastic Band (NEB) simulations
  6.7 The unified “middle” thermostat scheme in AMBER for efficient configurational sampling (ADVANCED)
  6.8 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
  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 Hen Egg-White Lysozyme
  8.2 Constant pH and Redox Potential MD example: predicting pH-dependent E^o values
  8.3 A simple coupled potential QM/MM/MD simulation.
  8.4 Steered molecular dynamics of a proton transfer reaction
  8.5 Quantum dynamical effects in liquid water: diffusion and IR spectra
  

• 9 NMR Refinement
  9.1 NMR Refinement of DNA and RNA Duplexes
  

• 10 Tools
  10.1 Unix and Editing Commands
  10.2 Building Systems - CHARMM-GUI
  10.3 VMD Visualization Software
  10.4 Chimera Visualization Software
  10.5 Plotting
  10.6 Jupyter Notebooks and Python
  10.7 Course Grain SIRAH