2024 AMBER tutorial 2 with PDBID 1NDV

Introduction

DOCK6 is a great tool that helps us understand ligand binding poses and relative binding energies. When DOCK6 is combined with another computational method known as molecular dynamics, we can calculate free energies of binding and probe how the ligand behaves in the binding pocket. In this tutorial we will walk through the use of AMBER16 to perform and analyze molecular dynamic simulations of PDBID 1NDV.

Getting Started

Before starting simulations it is important to create our directories so that we can keep our simulations organized. Create the following directories:

000.paramters
001.tleap_build
002.equilbration
003.production
004.analysis
zzz.master

We will use the zzz.master directory to store our initial mol2 files and other files we may use that do not belong in another directory. Once you have your directories created you can begin to prepare they system for simulation.

Before Simulation

Structure

We will need mol2 and pdb files of the ligand and receptor separately for these simulations. If you followed the 1NDV DOCK6 VS tutorial you will already have these files and can move them to the zzz.master directory, if not follow the steps below. Please note that the receptor file should be without charges and hydrogens, while the ligand will need the charges and hydrogens.

First open the PDB of 1NDV in Chimera. Now to select all the protein atoms we will