In this window we can adjust the representations of the protein, the ligand and the ions if needed. This will open the ‘Graphical Representations’ window. Close the ‘Molecule File Browser’ and go to: Now that we have loaded the topology and the 5074 frames, we can edit how the system will look. You should see the protein in the main VMD window (the windows with the name ‘VMD 1.9.3 OpenGL Display’). This means that the trajectory file that we are going to load is going to be linked with the topology file, hence the importance to read the prmtop file before the trajectory file.Ĭlick the load button to load the trajectory file. Make sure that the ‘Load files for:’ has the vph.prmtop topology selected. Now click the Browse button and select the trajectory file vph.nc. Load the vph.prmtop topology first! Select the file and click the Load button. With the topology and the trajectory file downloaded, go to: This tutorial has been prepared in an PC computer running the Linux Ubuntu operating system with VMD version 1.9.3. The topology file is vph.prmtop and the trajectory file is vph.nc. For this tutorial we are going to use a trajectory of a protein receptor that has a bound ligand in the active site. In this tutorial we are going to use the Visual Molecular Dynamics ‘VMD’ visualizer from developed at the University of Illinois at Urbana-Champaign. Movies are always useful to show a simulation. You want to generate a nice movie from your trajectory data. Making a movie from an AMBER trajectory using VMD
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