Difference between revisions of "2022 AMBER tutorial 1 with PDBID 6ME2"

Revision as of 22:18, 2 May 2022

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

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

Ligand File Generation

Generating Simulation Parameters

Using TLeap

Equilibrating the system

MD Production

MD Analysis

RMSD Calculation

Calculating Number of Hydrogen Bonds

MMGBSA Calculation