TUTORIAL B6 - SECTION 4
Using Sirius with AMBER
By Sasha Buzko
4) Working with AMBER output files
MD component of Sirius can load directly output (.out) files generated in a simulation. Just like the prmtop and mdcrd, output files can be either gzipped or uncompressed. Since an out file references the appropriate prmtop and mdcrd files, Sirius assumes that they all are located in the same directory. Also, since out files contain energy information, the changes in kinetic, potential and total energy can be displayed in a graph.
For this exercise, you will need the following files: step1.out.gz, step2.out.gz, 1NLN_ff03_no_disulphide.prmtop, step1.mdcrd.gz and step2.mdcrd.gz.
Clear the workspace and choose Open MD output file... from the File menu. In the file dialog, select step1.out.gz and step2.out.gz using Shift or Ctrl key, and click OK. The ordering dialog will appear, but since no reordering is needed in this case, just skip it by hitting Enter or OK button. Sirius will load the trajectory from both sequential files and display the structure corresponding to the first frame. To improve structure visibility, show a ribbon via the Show/hide ribbon... option in the Appearance menu of the main application window.
Since out files contain energy information, we can use it and display system changes in a graph. In the Data menu, check Show energy graph. A small panel with a graphical representation of energy will appear below the MD panel. Kinetic energy graph is displayed in black, potential energy - in blue, and total energy - in red. Now, when you start playback, a red line cursor will start moving along the graph showing the position of the current frame.
In addition to the graph, exact numeric values for the three energy components are given in the MD panel. They are updated at every frame and provide a real-time reference.
Keep this trajectory loaded for the next exercise in section 5.
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