AMBER Tutorials

The first two tutorials below are probably the best ones for those new to Amber.

• DNA
  Basic introduction to LEaP, sander, carnal and ptraj, to build, solvate, run MD and analyze trajectories.

• Plastocyanin/ion/water
  Basic tutorial for a protein, introducing non-standard residues, NMR restraints, and more complex modeling tasks.

• 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.

• Simple free energy example
  Follow a valine-to-alanine mutation in water.

• 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.

• Methane in water box
  Build methane, solvate, equilibrate and perturb.