VMD Tutorial

VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

Click here to learn more about VMD!

1. Load molecule

The first step is to download a molecule.Please download a pdb file (such as PDB id is 2HMB) from here(input the id ,and click,)and we will load this pdb file.

In "VMD Main" ,File -> NEW Molecule.

In "Molecule File Browser",Browse -> select pdb file.

In "Molecule File Browser", make sure "Determine file type" shows "PDB" from dropdown menu. It shouled be "PDB" automatically once you select a PDB file.

In "Molecule File Browser",click Load.

Now , the molecule display in "OpenGL Display"!

2. Display protein

To see the three-dimensional structure of a protein, we use a variety of mouse modes.

In "OpenGL Display" , Press move the mouse while holding the left mouse button, enter one step to observe what is happening. This is the mouse Rotation mode, through this mode, You can make this molecule around parallel axis rotation of the screen.

If you press the right mouse button, Repeat the previous step, The numerator will rotate around an axis perpendicular to the screen

In "VMD Main"-> Mouse, Here, you can change the mouse mode from "Rotation" to "Translation" or "Scale".

Translation Mode allows you to hold down the left mouse button Key to move molecules on the screen.

In Scale Mode, you can hold down the left button water move the mouse flat to zoom in or out.

3. Visualization of the structure

VMD can display your molecules in a variety of drawing modes. Here,we have to learn more about those that can help you drawing mode for different structures in proteins.

In "VMD Main",Graphics -> Representations,we can see the graphical representation of the molecules currently displayed(lines).

In "Graphical Representations", under "Selected Atoms", type in "resid 1 to 157". In "Coloring Method" drop down menu, choose "ColorID", then choose a color you prefer. In "Drawing Method" drop down menu, choose "New Cartoon". We should have E-selectin structure displayed with its secondary structure.

In "Graphical Representations", click "Create Rep". Under "Selected Atoms", type in “resid 158 to 162 and noh”. In "Coloring Method" drop down menu, choose "Name". In "Drawing Method" drop down menu, choose "Licorice". We should now have see displayed in stick model.

4. Obtain geometry information

	Query atom. In "VMD Main", Mouse -> Label -> Atoms. Then, click on the atom of interest. The label information of the atom should be displayed. For example "THR67:CG2", it means the atom belongs to THR residue, resid is 67, and atom name is "CG2".
	We know that the molecular structure involves the position of an atom in space, related to the type of chemical bond of the bond, including the bond length, the bond angle, and the dihedral angle between the three adjacent bonds.
	So in "VMD Main", Mouse -> Label -> Bonds/Angles/Dihedrals. Then, click the atoms the queried geometry in sequence, we can measure bond length/angle/dihedral.
	To overlay two structures for comparison,we need load a another molecule . Then click Extensions->Analysis->RMSD Calculator. In the RMSD Tool, change residues' range that you intrested to correspond to your correct protein residue range (i.e. residue 1 to 132) and click Align. This will align the two proteins along their backbone. (If you get an error when you try to align, try reducing the end of your residue range by 1 until it works.) To calculate a relative RMSD, click RMSD.

For more information of your queried geometry, In "VMD Main", Graphics -> Labels. In the Labels menu, choose the category the drop down on the left corner. Then, click on the geometry from the box below, its information should be displayed.

5. Visualization window adjustment

In "VMD Main", Display -> Orthographic

In "VMD Main", Display -> Axes -> Off

In "VMD Main", Display -> Depth Cueing

In "VMD Main", Extensions -> TK console -> type in "display resize 1000 800". This command resizes your VMD display window. It ensures the output image size ratio.