Lab 2, part 2/2: Visualization of molecules using VMD¶

The tasks below are part of Assignment 3. You can download it from OWL.

Create yourself a work directory (name it as you please; it may be good to put it under the course directory that you have already created and to use a descriptive name for the subdirectory).

Visualizations for the human islet polypetide are shown in Fig. 1.5 in the lecture material. Download the corresponding PDB file and try to recreate the visualizations as closely as possible. Which ones are the most informative? Use Tachyon rending to produce a high-quality image as discussed in the VMD section.

For tasks 2-5 do the following: The VMD section of lecture material contains an example of .gro file that contains 5 water molecules.

Create yourself a work directory (name it as you please; it may be good to put it under the course directory that you have already created and to use a descriptive name for the subdirectory) for this part and create a file called spc5.gro in there.

Once done, open the file in VMD. If you encounter problems, first examine very carefully that the file is exactly in the format as given in the example.

Try to recreate the visualization shown in the lecture notes in connection with the file (Inside the Example of the .gro format tab). For this, you will have to try different representations for the molecule. Then render the molecule. Use Tachyon rending to produce a high-quality image as discussed in the VMD section.
Color each of the oxygens with a different arbitrary color and render.
Use a different representation for each of the water molecules and render.
List all the residue names, names and elements present in the system.
Examine the keywords residue and resid. What is the difference between them?

CHEM3300G

Lab 2, part 2/2: Visualization of molecules using VMD¶