2022 AMBER tutorial 1 with PDBID 6ME2
- 1 Introduction
- 2 Directory Setup
- 3 6ME2 Structure Files
- 4 Generating Simulation Parameters
- 5 Using TLeap
- 6 Equilibrating the system
- 7 MD Production
- 8 MD Analysis
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.
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
If the 6ME2 DOCK tutorials were followed before this AMBER tutorial, the user has some experience generating and prepping receptor and ligand filed from the original 6ME2 PDB file. However, it is recommended that the user NOT use the files generated in the 6ME2 DOCK tutorials and start from scratch here, as this allows the chance to catch mistakes that may have been made but not recognized while following the initial DOCK tutorials.
To begin this tutorial, search the Protein Data Bank (PDB) website using the code 6ME2, or use the Fetch... button on the home screen of UCSF Chimera for this four-letter code.
Receptor File Generation
To generate a fresh copy of the receptor file, open the