What we need to do is to ensure that all of the frames from both trajectories are aligned against a common frame of reference. This makes comparison of the two trajectories difficult. You should be able to see that the molecules in h7n9_rk.pdb are not aligned with those in h7n9.pdb, and so oseltamivir in h7n9_rk.pdb appears rotated by about 90 degrees compared to oseltamivir in h7n9.pdb. Once you have done this, zoom in to get a view similar to that in the above picture. To do this, you will need to ensure that the “Selected Molecule” selector at the top of the “Graphical Representations” window is selecting “2: h7n9_rk.pdb”, e.g. Go into the graphical representations window and add representations to match those for h7n9.pdb. The molecules in h7n9_rk.pdb are currently visualised using the “lines” representation. Select this and click “Load” to load this file. Then click “Browse” and find the h7n9_rk.dcd file that you downloaded. To do this, in the “Molecule File Browser” window change the “Load files for:” selector to select “2: h7n9_rk.pdb”. Next, we will load the trajectory in h7n9_rk.dcd into the molecules loaded from h7n9_rk.pdb. Then, ensuring that the “Load files for:” selector is selecting “New Molecule”, click “Browse” and find the h7n9_rk.pdb file that you downloaded. To do this, click “File | New Molecule…” in the VMD main window to open the “Molecule File Browser” window. Next, we will load up the h7n9_rk.pdb file in addition to the h7n9.pdb file that is already loaded into your VMD session. h7n9_rk.dcd : This contains the trajectory from a 50 nanosecond molecular dynamics simulation of oseltamivir bound to the R292K mutant of H7N9 neuraminidase.h7n9_rk.pdb : This is a PDB file containing oseltamivir bound to the R292K mutant of H7N9 neuraminidase.Please download the below two files and place them into the same directory as h7n9.pdb and h7n9.dcd
Vmd movie rotate and trajectory how to#
The final thing we will learn in VMD is how to load up and compare the output of two different molecular dynamics trajectories. Part 1: Molecular Visualisation Comparing Trajectories Molecular Visualisation, Modelling and Dynamics.Sampling the Ligand - Intramolecular Moves.Sampling the Solvent - Rigid Body Moves.Part 2: Parallel Programming Using Intel Threading Building Blocks.Concepts, Default Arguments and Operators.
Vmd movie rotate and trajectory software#
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