![]() ![]() Our molecules are ready, but we need to adjust a couple of more option before rendering our movie. Hit the play button and the animation will now run quite smooth. We can change between each by clicking in the Graphical representations list of molecules. We have to do this for the ligand and for the protein. Click on the ‘Trajectory’ tab and apply a ‘Trajectory Smoothing Window Size:’ of 3. ![]() To smooth the animation, we can use the ‘Trajectory Smoothing’ option. Saving too often does make the animations smoother, but the trajectory files are extremely big and not very convenient. This is because of the frequency of saving trajectory data when we are running the simulations. If we hit play to preview the movie, we notice that the animation is not smooth and that is very ‘bumpy’. To go back to 3D rotation, hit the ‘r’ again. If you type the ‘s’ letter, you can scale (zoom in and zoom out) and with the ‘t’ you can translate the system. You can switch between 3D rotation mode by hitting the ‘r’ letter in the keyboard. Click on the OpenGL Display and use the mouse to rotate the 3D perspective of our system. We can visualize the movie with this new representations of the ligand and the protein by clicking on the play button in the ‘VMD Main’ window, and we can use the mouse to adjust the perspective of our system. Since we made a copy of the protein’s representation, the Material is still showing the AOEdgy material, which is what we want. We can clearly see the ligand docked in the active site of the protein. Select Name as the Coloring Method and VDW as the Drawing Method. In our case, we only have one residue with that name, which will appear in VMD’s main window. This will select all residues that have the name ‘LIG’. In the ‘Selected Atoms’ field, delete ‘protein’ and type: resname LIG This will copy the current representation that we have, that we will use as a template for the ligand. Click on the ‘Create Rep’ button in the Graphical Representations window. To select the ligand and change the representation, we need to add a new representation. This material makes the overall representation more bright and also will make use of a special render engine available in VMD as we will see in the next steps. In the Material drop-down menu, select: AOEdgy In order to enhance our movie, we are going to change the Material that we are using to add color to the structure. With this coloring method, each secondary structure will be colored by a different color, which highlights each region accordingly. In the ‘Coloring Method’ drop-down menu, select: Secondary Structure Let us change the color to enhance these features. This will change the representation of the protein for a more easier visualization were alpha helices and beta sheets are easier to distinguish. In the ‘Drawing Method’ menu, click and select: NewCartoon Now let us choose a better representation for the protein. This will select only the atoms that are included in the protein. In the ‘Selected Atoms’ field, delete the word ‘all’ write the word protein. To do this, we have to select the protein only. We will use different methods of visual representation for the protein and the ligand. 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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