Revision as of 10:44, 9 March 2023

Introduction

AMBER is a molecular dynamics program that can be run on your protein/ligand complex to ensure that the interactions between the two structures are stable. DOCK shows us how the two interact with each other at one point in time. AMBER looks at those interactions over time to ensure that forces will not occur which will push the ligand out of the binding site as the complex naturally moves. This tutorial will again be working with PDB #4s0v

Setting Up Your Environment

Just as with DOCK you should set up for directory structure at this point to keep everything organized and easy to find. We will be creating a new structure which looks like:

Structure

Before starting the analysis it's best to download a new protein/ligand complex from the PDB and isolate both the protein and ligand structures. Follow the steps in the *[1] tutorial to do this. The inputs we need are the isolated protein with NO hydrogens and NO charges; and the ligand with hydrogens and charges. In other words, once you isolate the protein structure in Chimera, save it with a filename such as, 4s0v_protein_for_AMBER.pdb. Then isolate the ligand structure, add hydrogens and re-do whatever protonation changes you made in the *[2] tutorial. Once the protonation state is correct, add charges and save the file as 4s0v_ligand_for_AMBER.mol2.

Once these two files have been generated, scp them over to the 001.structure directory on Seawulf.

Force Field Parameters

AMBER needs force field parameters to run correctly. This only needs to be done for the ligand since information about the protein has been done over previous years. To generate the necessary files for AMBER we will be working on the command line on Seawulf, please cd into your 002.forceFieldParameters directory.

To generate the parameters for the ligand type in the following command:

 antechamber -i ../001.structure/4s0v_ligand_for_AMBER.mol2 -fi mol2 -o 4s0v_ligand_antechamber.mol2 -fo mol2 -at gaff2 -c bcc -rn LIG -nc 0

The important parameter in the above command is the -nc option at the end. This is telling antechamber what the total charge is on your ligand. This number needs to be the same as the number used in the previous step when you added charges to the structure in Chimera.

TLeap Implemenation

Complex Minimization and Equilibration