Part 1: Molecular Visualisation

Molecular Movies

In addition to being useful for viewing 3D structures of static biomolecules, VMD can also be used to create movies of the output of molecular dynamics simulations. Molecular dynamics (MD) is a simulation technique that adds motion to computer models of biomolecules. MD works by calculating the forces that result from the interactions between atoms (e.g. electrostatic attraction and repulsion, interatomic van der Waals interactions, bonded interactions). These forces are calculated for every atom in each molecule in a biomolecular system, and used to work out how each atom would move over time. The result is a molecular dynamics trajectory, which can be used to produce a movie that approximates the motion of the complete biomolecular system.

A molecular dynamics simulation of H7N9 neuraminidase bound to oseltamivir was performed and is described in the paper on which this workshop is based. This resulted in a molecular dynamics trajectory file, h7n9.dcd, which can be downloaded here. Please download this file and put it into the same directory as h7n9.pdb.

We want to start in a new VMD session, so close you current session by clicking “File | Quit”. Then, once VMD has exited, start a new session by typing

vmd

at the shell prompt in a terminal window.

Now, load up the h7n9.pdb file using the same procedure as before (click “File | New Molecule…” to open the “Molecule File Browser”, then click “Browse…” to find the h7n9.pdb file, then click “Load” to load the PDB).

Now that we have loaded h7n9.pdb, we need to load the molecular dynamics trajectory for this molecule into this view. We do this by clicking “Browse” again in the “Molecule File Browser” and this time selecting h7n9.dcd, e.g. as below;

Image showing molecule file browser to load trajectory

Note that VMD has already worked out that this file has a file type of “CHARMM,NAMD,XPLOR DCD Trajectory” and that this option has been selected in the “Determine file type:” selector. If VMD has not selected this option, then please make sure that this is selected (you will see that there are a large number of different molecular file formats!).

Next, you need to ensure that the trajectory will be loaded into the molecules loaded from h7n9.pdb. To do this, ensure that the “Load files for:” selector is selecting “1: h7n9.pdb”. This will ensure that the molecular trajectory that you load will be added to the molecules loaded from h7n9.pdb. Once everything is ok, click “Load” to load the molecular dynamics trajectory from h7n9.dcd.

Once you’ve clicked “Load” you will see the molecules in the VMD graphics window animate as each of the 500 frames from the molecular dynamics trajectory are loaded. Once loaded, you should have a screen that looks like this;

Image showing window after loading trajectory

There are several controls and pieces of information that are now available for the loaded trajectory;

Now that the molecular dynamics trajectory is loaded you need to add some graphical representations to the molecule so that you can get a better view of what occured during the trajectory. Open the graphical representations window and add these representations;

Also, change the color of the background to white and turn off the display of the axes. Then rotate and zoom in the view until you have a good view of oseltamivir in the binding site of H7N9 neuraminidase. Once you have done all of this, you should have a view like this;

Image showing window after loading trajectory

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