AMBER Tutorials

The first two items below are probably the best ones for those new to Amber. The remaining tutorials are those included with the Amber 8 release.

• Beginning Amber Workshop,  prepared by Ross Walker.
  This is an online workshop containing a total of ten tutorials that cover basic simulations, estimating binding enegies and pKa values, treating non-standard residues or arbitrary organic molecules as ligands, simple QM/MM simulations, Nudged Elastic Band Simulations, and using VMD for visualising AMBER simulations and a case study on TRP-Cage folding that includes advanced trajectory analysis (RMSD, Hydrogen Bonds, Cluster Analysis and Torsion angle tracking). If you are new to AMBER this is the place to start as the tutorials will step you through all of the various stages involved in running MD simulations using the AMBER software suite. These tutorials are regularly updated and should be your first point of call for learning how to use AMBER. Coming soon... A tutorial on installing AMBER on Linux Machines (Serial and Parallel) and on Windows machines using cygwin.

  

• PSC 2005 Workshop tutorials,  These were prepared for a June, 2005 workshop at the Pittsburgh Supercompter Center, (see photo at right), and cover basic simulations, peptide folding, computing free enegies and pKa values, and treating non-standard residues or arbitrary organic molecules as ligands. Some of these tutorials are repeats or updated versions of those listed in the Beginning Amber Workshop above, or those listed below. Three, however, are completely new.

• MM-PBSA tutorials, prepared by Bethany Kormos and Dave Beveridge. There are separate files (PDF) for version 7 and for versions 8 and 9.

• DNA By Ross Walker, based on the original DNA tutorial by Thomas Cheatham.
  Basic introduction to LEaP, sander and ptraj, to build, solvate, run MD and analyze trajectories. Also covers visualising of trajectories using VMD.

• Loop dynamics of the HIV-1 integrase core domain (from Matt Lee, Univ. of Delaware)
  Walk-through of a yet more complex study of protein dynamics.

• NMR refinement of a DNA duplex
  Basic introduction to NMR refinement using LEaP and sander.

• Generalized Born solvent model
  Carry out a protein simulation with a continuum solvent model.

• Streptavidin/biotin complex, partially solvated
  Build biotin, load complex, partially solvate, equilibrate dynamics.

• Crown ether in vacuum
  Build crown molecule, explore dynamics, perturb complexed ion, and analyze it all. Consideration given to energy conservation, equipartition, timestep, SHAKE.

• Simple demo of ptraj commands
  Analyze a peptide simulation to gather a variety of statistics

• Thermodynamic integration
  Estimate the free energy of converting toluene to nothing, in water. Compare the results to literature values.