2022 AMBER tutorial 1 with PDBID 6ME2

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Revision as of 23:07, 2 May 2022 by Stonybrook (talk | contribs) (Directory Setup)
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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