View source for 2022 AMBER tutorial 1 with PDBID 6ME2

== '''Introduction''' ==

AMBER is a program designed for computing biomolecular simulations. In this tutorial, AMBER will be used to simulate the dynamics between the ligand and receptor of the 6ME2 PDB file.

== '''Directory Setup''' ==
For this tutorial, it is recommended to define the following directories to stay organized:

  mkdir 001_structure
  mkdir 002_parameters
  mkdir 003_leap
  mkdir 004_equil
  mkdir 005_production

== '''6ME2 Structure Files''' ==

=== '''Receptor File Generation''' ===

=== '''Ligand File Generation''' ===

== '''Generating Simulation Parameters''' ==

== '''Using TLeap''' ==

== '''Equilibrating the system''' ==

== '''MD Production''' ==

== '''MD Analysis''' ==

=== '''RMSD Calculation''' ===

=== '''Calculating Number of Hydrogen Bonds''' ===

=== '''MMGBSA Calculation''' ===