TUTORIAL B6 - SECTION 3
Using Sirius with AMBER
By Sasha Buzko
3) Opening MD visualization module and loading AMBER trajectory data
Open Sirius or clear the workspace of any loaded data by selecting Close all entries from the File menu of the main window or by clicking the corresponding toolbar button. Open the MD module by selecting Molecular Dynamics Panel from the Viewers menu. The MD panel will be displayed on the right from the main window. The panel has three main areas: information about loaded data (top), playback controls (middle) and parameters of the run (bottom).
The MD module reads parameter files (prmtop) followed by trajectory (mdcrd) or single frame files (inpcrd, rst). Coordinate files are directly loaded in uncompressed or compressed form (gzipped). In addition, Sirius accepts output files from AMBER simulations that refer to the prmtop and mdcrd files located in the same directory. Once again, any of the data files may be gzipped.
All menu items and buttons from now on refer to the MD panel. First, let's load a single snapshot using prmtop and inpcrd files. These are the files you will need: polyAT_vac.prmtop and polyAT_vac.inpcrd. First, click File -> Open parameter file... Make sure the pulldown menu "Files of type" shows "Amber parameter File". Select polyAT_vac.prmtop and click OK. The Parameter file line will display the name of the loaded file. Next, select File-> Open coordinate/trajectory file... and select polyAT_vac.inpcrd. A DNA structure is then displayed in the 3D workspace and descriptive information is shown in the Loaded data area of the MD panel. Frame count should show 1.
Sirius also reads restart files. Clear the data from the display by selecting File->Clear data. Then load the same prmtop file, followed by polyAT_vac_init_min.rst.
Now we will load a trajectory file using a prmtop and a single gzipped mdcrd file. Clear any loaded data from the workspace by selecting File->Clear data in the MD panel or File->Close all entries in the main window. You will need the following files: polyAT_vac.prmtop and polyAT_vac_md1_12Acut.mdcrd.gz. First, load the prmtop file. Next, open the gzipped trajectory file using the Load coordinate/trajectory file from the File menu. Check correctness of the loaded data: atom count should be 638 and frame count is 1000.
Start trajectory playback by clicking the Play button in the "Play MD trajectory" area of the MD panel. Playback can be paused by clicking Stop or returned to the first frame by clicking Reset. You can also step through the frames one by one in either direction using the forward and backward arrow buttons under the frame counter.
While the trajectory is played, the structure can be freely rotated, translated and zoomed in or out. Speed of the playback can be adjusted using the slider in the lower right part of the MD panel. This can be done during the playback.
Next, we will load a trajectory that spans several mdcrd files, which is frequently the case for large simulations. Files used in this example are TC5b.prmtop, heat1.mdcrd.gz,heat2.mdcrd.gz and heat3.mdcrd.gz. Clear the workspace and load the TC5b.prmtop file. Then, in the same coordinate/trajectory loading dialog, select all three of gzipped mdcrd files using Ctrl or Shift key. Click OK. Next, a window with a list of selected files will appear. Since the filesystem does not necessarily list files in the same order as they were saved in the simulation, you can use this dialog to rearrange them with Move up and Move down buttons that move the currently selected file. In this particular case, no reordering is needed, so simply click OK. Atom count should be 304 and frame count should be 600. To improve visibility of the peptide backbone, show the ribbon (in main window: Appearance->Show/hide ribbon).
Practice with playback using play/stop/reset combinations. Note that in the stopped position, the frame location slider can be dragged to any desired frame within the trajectory. When playback is started again, it will resume from the new position.
Sirius supports a variety of geometry-related operations, such as measurements of distance, bond angles and dihedral angles. In addition, you can detect hydrogen bonds and steric clashes that may be present in the structure. These features can be accessed from the Geometry menu of the main window. Distance/angle measurements are straightforward, and are done by clicking the corresponding atoms in the 3D workspace. For hydrogen bonds, use Geometry->Detect hydrogen bonds. For internal hydrogen bonds, leave the default selection of "Type of hydrogen bond detection". Then specify which set of atoms should be analyzed for presence of hydrogen bonds. The default is current selection. For the entire structure, choose its name from the pulldown menu. Maximum distance between the heavy atom and the hydrogen can be specified in the corresponding text field.
For details on using these features, please refer to other tutorials provided on the Sirius web site.
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