Part 3: Mutating Proteins and MD Setup

Getting Started

To start, we must first download the files that you will need for this section of the workshop. You can download the files here (mutation.tgz).

Change into the directory in which you have downloaded mutation.tgz and unpack it using the command

tar -zxvf mutation.tgz

This will create a directory called ‘mutation’. Change into this directory by typing;

cd mutation

If you look in this directory you will see the following files;

:-> ls
1NNC.pdb     ZAN.frcmod   ZAN.prepin   add_atoms.in add_water.in ca.frcmod    ca.prep      equilconfig  heatconfig   mdconfig     minconfig

There are a lot of files. The first one we will look at is ‘1NNC.pdb’. This is a PDB file of zanamivir bound to the wild type form of H7N9 neuraminidase. You can look at this file by typing;

vmd 1NNC.pdb

Image showing 1NNC

You will see that the protein and zanamivir are missing hydrogen atoms, and that this is not in a box of water. You can view zanamivir by creating a graphical representation using selection string “resname ZAN”. You can view arginine 292 by creating a graphical representation using selection string “resid 292”.

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