Animate secondary structure vmd12/31/2023 Make sure "1: ubiquitin.psf" is the selected molecule. First hide 1UBQ.pdb by double clicking it's D attribute in the main window. Once you are finished we will set up a representation that will make viewing the trajectory most informative. Play around with the animation controls to get a feel for them. Speed Slider - drag to left for slower animation speed, right for faster animation speed.Step Size - specify the number of frames to jump when using the animation controls.Loop Control - specify looping behavior for the trajectory animation.Trajectory Bar - Click and drag to move through the trajectory.Frame Number - Type in a frame number and press enter to jump to that frame.The animation controls are all located at the bottom of the main window. Now we will discuss the animation controls. Now browse for your trajectory file (pulling.dsd) and click load. Make sure the Load files for dropdown says "1: ubiquitin.psf". Now, you will load the trajectory into the current molecule. Next, load ubiquitin.psf as a new molecule (Click the Load files for dropdown and select New Molecule). Click Browse, open 1UBQ.PDB, and click load. Once you have the files, start VMD and open the Molecule File Browser under the File menu. pulling the protein apart by applying a force to one end). This trajectory is of simulated unfolding of ubiquitin via atomic force microscopy (i.e. It contains protein coordinates that change as a function of time. pulling.dcd (29M) - This is a NAMD trajectory file.It contains the coordinates of our protein molecule as well as the way in which bonds are formed. ubiquitin.psf (2M) - This is a topology file. ![]() It will not be used apart from the fact that it is needed to load the topology file and the trajectory file. 1UQB.pdb (49K) - This is the PDB file of the x-ray structure of ubiquitin.You may be wondering, "If I'm using their files, why you shouldn't I be using their tutorial instead of this one?" The answer is that their tutorial is a bit out of date and uses complex Tcl commands that can be circumvented with the GUI in the newer VMD versions.įirst you will need to download three files: For this tutorial we will use a NAMD trajectory that was part of the VMD tutorial on their site. Here we will learn to use VMD to examine a trajectory the same way we used it to examine a static structure in the Representations section. One of the great strengths of VMD is its ability to view trajectories from various molecular dynamics software packages (including Gromacs, Tinker, NAMD, XPLOR, AMBER, etc.). Viewing Trajectories Viewing Trajectories
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