![]() You are encouraged to take a look at that file using a text editor. vmd file you saved in Basic Protocol 1, step 47, is actually a series of commands. There are six lines in this file, and each line represents a Tcl command line that you have used before. Using any text editor of your choice, open the file beta.tcl. Take a quick look at the script beta.tcl. The blue residues are the LYS and GLY residues in the ubiquitin. You should see that the protein is mostly a collection of red spheres, with some residues shown in blue. In the Tk Console window, type sourcebeta.tcl and observe the color change. The script beta.tcl sets the colors of residues LYS and GLY to a different color from the rest of the protein by assigning them a different beta value, a trick you have already learned in Basic Protocol 6, steps 5–9. You should have downloaded a simple script, beta.tcl, with this unit. Just use any text editor to write your script file, and in a VMD session, use the command source filename to execute the file. When performing a task that requires many lines of commands, instead of typing each line in the Tk Console window, it is usually more convenient to write all the lines into a script file and load it into VMD. Thus, $crystal is now a function that performs actions on the contents of the “all” selection. This concept is particularly important when multiple molecules are loaded at the same time (see Basic Protocol 9 for dealing with multiple molecules in VMD). A top molecule means that it is the target for scripting commands. Instead of a molecule ID (which is a number), we have used the shortcut “top” to refer to the top molecule. This step creates a selection, crystal, that contains all the atoms in the molecule and assigns it to the variable crystal. The selection returned by atomselect is itself a command you will learn to use. The first argument to atomselect is the molecule ID (shown to the very left of the VMD Main window), the second argument is a textual atom selection like what you have been using to describe graphical representations in Basic Protocol 1. This command allows you to select a specific part of a molecule. Type set crystal in the Tk Console window. If you are using a Mac, your vmd console window is the terminal window that shows up when you open VMD.Ģ. The Tcl commands that you enter in the VMD TkConsole window can also be entered in the vmd console window. It should tell you a molecule has been loaded, as well as some of its basic properties like number of atoms, bonds, residues and etc. The vmd console window tells you what’s going on within the VMD session that you are working on. When you open VMD, by default a vmd console window appears. You can use the standard Unix commands in the VMD TkConsole window to navigate to the correct directory. If you see the error message ”Unable to load file ‘1ubq.pdb’ using file type ‘pdb’”, you might not be in the correct directory that contains the file 1ubq.pdb. In the VMD TkConsole window, type the command mol new 1ubq.pdb and hit enter.Īs you can see, this command performs the same function as described at the beginning of Basic Protocol 1, namely, loading a new molecule with file name 1ubq.pdb. If you give me your email I will send you two figures with a sample of the projections on eigenvectors 1 -10. Unfortunately, I am told that as a “new user” I cannot upload attachments (?). (iv) The projections of the trajectory on the first six eigenvectors are abnormally large, but the amplitude of their oscillation is smaller than that of the projection on the following “well-behaved” normal modes. The first ten eigenvalues are as follows: 1 -0.0392398 (iii) The eigenvalues of the first six eigenvectors are small. This should be used for ‘Normal Modes’ analysis”. From the Gromacs manual, nmeig module: “-m Divide elements of Hessian by product of sqrt(mass) of involved atoms prior to diagonalization. I tried to have the eigenvectors computed non mass-weighted, with the option -nom, but apparently nmeig assumes always the option -m. Also the first six eigenvectors have norms in that range. (ii) The eigenvectors produced by nmeig are (almost) orthogonal, but NOT normalized: their norm is in the range 0.37 - 0.40 u^0.5 nm, because nmeig computes them mass-weighted in default. As a matter of fact, the unfiltered and filtered 10 ns trajectories I am using are almost equal, the roto-translational motion is negligible (the translational motion had already been compensated for during the computation of the trajectory). (i) I filter the trajectory to eliminate the roto-translational movement of the protein because I am interested in analysing the energy exchange among internal vibrational degrees of freedom of the protein. ![]()
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