AMBER Free Energy Workshop

Welcome to AMBER free energy workshop tutorial page.
Below are the links for the tutorials for each day and session:

Day 1

Session 1

  • Visualization and basic analysis of AMBER simulations: Quick start for VMD & cpptraj

    • Day 2

    Session 2

  • Building and simulating MTR1 enzyme substrate complex

    • Session 3

  • Non-standard residue parametrization: MTR1 ligand
  • Non-standard residue parametrization: acetic acid
  • Non-standard residue parametrization: TYK2 ligands

    • Day 3

    Session 4

  • QM/MM simulations to study MTR1 reaction.

    • Day 4

    Session 5

  • Alchemical free energy calculations for acetic acid.
  • Alchemical free energy calculations for TYK2 ligands

    • Day 5

    Session 6

  • MM to QM/MM bookending with acetic acid.
  • gwTP with MTR1.