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Amber Tutorials

Here are a number of tutorials prepared by the AMBER developers to help you in learning how to use the AMBER software suite. Clicking on each chapter heading will take you to a new page of abstracts on each of the topics linked in this Table of Contents. If you can see what you want from the titles, you may go directly to each tutorial from here.

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• Introductory tutorials
  Learning the Unix Command-line
  Fundamentals of LEAP
  An introduction to molecular dynamics simulations with AMBER
  Simulating a small fragment of DNA
  Using VMD with AMBER

• Intermediate tutorials for common applications of Amber
  A case study in folding Trp-Cage (advanced analysis and clustering)
  Loop dynamics of the HIV-1 integrase core domain
  

• Creating special systems in AMBER
  Simulating the Green Fluorescent Protein and building a modified amino acid residue
  Setting up a system with the AMBER Lipid14 force field for bilayers and micelles
  Simulation of a protein crystal
  Simulation of a room-temperature ionic liquid
  Material systems modeling tutorial
  Using 3D-RISM to place waters
  

• Techniques for expedited sampling
  Simple replica exchange (REMD)
  Conformational equilibria of the poly-proline pentamer by Steered MD (SMD) and REMD
  Using Accelerated Molecular Dynamics (aMD) to enhance sampling
  Adaptive Steered Molecular Dynamics
  Conformational equilibria of methyl-alpha-L-iduronic acid by basin flooding
  Nudged Elastic Band (NEB) simulations

• Computing free energies in AMBER
  Molecular Mechanics with a Poisson‐Boltzmann/Surface Area solvent: MM-PBSA
  pKa Calculations using Thermodynamic Integration
  Thermodynamic Integration using soft core potentials
  Umbrella sampling: A Potential of Mean Force in alanine dipeptide Phi/Psi rotation
  Free energy estimation for conformers of dialanine using EMIL
  Computing binding enthalpy values
  Free energy calculations with the Free Energy Workflow Tool (FEW)
  Grid Inhomogeneous Solvation Theory for water thermodynamics: in Factor Xa
  Computing Binding Free Energy using the Attach-Pull-Release (APR) Method
  The Nonequilibrium Free Energy (NFE) Toolkit for pmemd
  (Deprecated) Thermodynamic Integration using older sander techniques
  

• Trajectory analysis
  An Introduction to CPPTRAJ
  RMSD Analysis in CPPTRAJ
  Analysis of Nucleic Acid Simulations
  Introduction to Principal Component Analysis with CPPTRAJ
  Combined Clustering Analysis with CPPTRAJ
  Hydrogen Bond Analysis with CPPTRAJ
  An Introduction to PYTRAJ
  Simulating Crystals with AMBER on Jupyter notebook
  Using Jupyter notebook remotely
  Using NGLView for protein visualization in Jupyter notebook
  Trajectory rendering and movie making with NGLView
  Real time molecular dynamics simulation and visualization
  

• Extending the AMBER force field
  Modeling a drug compound using antechamber and the Generalized Amber Force Field
  Setting up a DNA-Ligand System with RESP charge fitting
  (Deprecated) Building your own custom residues
  Metal ion modeling with the Metal Center Parameter Builder
  Generating custom force field parameters with Paramfit
  Deriving Implicitly Polarized Charges in mdgx
  Deriving bonded parameters with mdgx
  

• Modeling chemical reactions and equilibria in AMBER
  Constant pH MD example: Calculating pK_as for titratable side chains in Hen Egg-White Lysozyme
  Constant pH and Redox Potential MD example: predicting pH-dependent E^o values
  A simple coupled potential QM/MM/MD simulation.
  Steered molecular dynamics of a proton transfer reaction
  Quantum dynamical effects in liquid water: diffusion and IR spectra
  

• Structure refinement in AMBER
  NMR Refinement of DNA and RNA Duplexes
  

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.