Difference between revisions of "2021 AMBER tutorial 1 with PDBID 1HW9"

Revision as of 23:29, 6 May 2021

Introduction

In this tutorial, we'll be exploring the wonders of molecular dynamics through the use of AMBER 16. AMBER 16 we'll help study the binding characteristics of the ligand to the target protein!

Directory Setup

It's important to stay organized during this process as we'll be generating a number of files during the process. Overall, we'll be working within five directories. They should be created as follows:

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

Before proceeding, double-check that all directories have correctly been made.

1HW9 Structures

Let's move into our directory titled 001_structure.

cd 001_structure

Receptor

We need to retrieve a fresh copy of the receptor before proceeding forward. Even if you've done the DOCK tutorial, you should still retrieve a fresh .pdb just in case Chimera did something wrong during the preparation process. In order to do so, head over to the PDB website and type in 1HW9 into the header. It should take you straight to the webpage. Download the system as a pdb and open it in Chimera. Our focus will be on Chain A of the complex. In order to visualize the chain:

 Select -> Chain -> A

Notice, however, that this does not remove Chains B, C, and D from our view. We need to perform this action manually.

 Select -> Invert (Selected Molecules) -> Actions -> Atoms/Bonds -> Delete

After deletion, the only thing remaining should be Chain A of the original file. It is within your best interest to save this session as you'll need to come back to this file when preparing the ligand. Doing so will prevent you from having to do the above deletion step again.

 File -> Save Session As ->

Now that the session has been saved, we can go ahead and isolate the receptor. While we've isolated Chain A, you'll notice that Simvastatin is still located on the molecule. In order to remove everything besides HMGR, we need to do the following:

 Select -> Residue -> ADP -> Actions -> Atoms/Bonds -> Delete
 Select -> Residue -> HOH -> Actions -> Atoms/Bonds -> Delete
 Select -> Residue -> SIM -> Actions -> Atoms/Bonds -> Delete

With the receptor isolated, go ahead and save the file as

1HW9_fresh.pdb