Part 3: Mutating Proteins and MD Setup

Comparing Trajectories

In this part of the workshop you have set up and are running a long molecular dynamics simulation of zanamivir binding to mutant H7N9-R292K neuraminidase. At the end of the last part you ran a long molecular dynamics simulation of zanamivir binding to wild type H7N9 neuraminidase. In this last section of the workshop you will look at the two trajectories from these simulations and will use VMD to compare them to see whether or not the R292K mutation affects binding.

First, we will look at the wild type simulation. Change into the directory containing the output from your wild type simulation, e.g. by using;

cd $HOME/dynamics/complex

assuming that the wild type simulation was run in the directory “$HOME/dynamics/complex”.

(or, if you didn’t have time to run the simulation, or if something went wrong, you can download example output here. Unpack the example output using the command “tar -zxvf example_dynamics.tgz”).

Once you have changed into the “dynamics/complex” directory, type;

vmd h7n9_zan.prmtop output.dcd

Create graphical representations that highlight neuraminidase, zanamivir and arginine 292 (resid 212), e.g.

Image showing wild type trajectory

Next, we will look at your mutant H7N9-R292K simulation. We will load this into the same VMD session as the wildtype.

Image showing file selector

Once you have loaded the trajectory create graphical representations that highlight neuraminidase, zanamivir and lysine 292 (resid 212), e.g.

Image showing file selector

If you zoom out, you should see that the trajectories from both the H7N9 and H7N9-R292K simulations have been loaded, but that the proteins are not aligned.

Image showing unaligned proteins

Image showing RMSD trajectory tool

Once you have aligned both trajectory, play the movies.

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