TUTORIAL B6 - SECTION 5
Using Sirius with AMBER
By Sasha Buzko
5) Computing RMSD
MD component of Sirius provides a flexible way to calculate root mean square deviation along the loaded trajectory. In addition, change of RMSD is represented graphically with a sliding position cursor indicating the currently displayed frame.
You can use the loaded trajectory from the previous section or repeat the loading process if the workspace is empty. With the data loaded and structure displayed, click Compute RMSD graph... in the Data menu of the MD panel. Use the dialog box to enter two required parameters. First, what should be considered the reference for RMSD calculation: the first frame of the loaded trajectory (default) or another structure of the same protein. In the second case, you can browse for a structure in PDB format. Second, you can choose which atoms are used to compute the RMSD. In some cases, only a specific part of the structure is of interest. Also, solvent molecules may need to be omitted, etc. The dialog presents several options:
All options except the last one are fairly self-explanatory, so let's use them first. Leave First frame of the run as the reference and select Use all atoms except solvent, then click OK. After several seconds, a new panel with the RMSD graph will appear under the main MD panel. The vertical scale represents RMSD values in Angstroms, and horizontal scale shows time, if available (for instance, output files contain time information).
When the trajectory is played, a red line cursor moves along the graph indicating the current position. If you repeat the RMSD calculation with different parameters (for example, use only alpha-carbons), the graph will update while the trajectory is being played back. Note differences in the vertical scale that reflect different extent of motion associated with more rigid parts of the structure (such as the protein backbone or alpha-carbons, as opposed to the full atom set).
Now we will use one of the features of the Sirius environment - ability to define atom sets. With the same trajectory loaded, open Sequence Viewer by selecting Sequence Viewer from the Viewers menu of the main application window. Using Shift key, select a range of residues in the Sequence Viewer (click a residue, press and hold Shift, and click the residue on the other end of the desired range). Selected substructure will become highlighted in the 3D workspace as well. Next, select Define/edit atom set... from the Structure menu of the main window. Type in any desired name (for example, "Set1") in the blank field next to "Create new set", leave "Use current selection" option on and click OK.
This operation has created a named set of atoms that from now on can be used in any operation, such as coloring, rendering, hide/show or RMSD calculation. For illustrative purposes, let's color the set blue. Select Structure color... from the Appearance menu (or click the corresponding toolbar button), click a blue rectangle in the color selection palette, and from the pulldown menu on the left side, select "Set1" (or whatever name you gave to your set). This will apply selected color only to the set you have selected.
Next, we'll go back to the MD panel and open Compute RMSD graph dialog again. This time, Use custom atom set option is enabled. Select it, choose "Set 1" from the pulldown menu next to it and click OK. This will recompute the RMSD for only the atoms that are part of the Set 1 and update the RMSD graph accordingly.
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