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Receptor Grid Generation Panel |
The Receptor Grid Generation panel is used to specify a receptor structure and set up the grid generation job. This job creates the grid files, which represent the active site of the receptor for Glide ligand docking jobs.
To open the Receptor Grid Generation panel, you can:
Choose Applications → CombiGlide → Receptor Grid Generation in the main window.
Choose Applications → Glide → Receptor Grid Generation in the main window.
Choose Tasks → Docking → Grid Generation in the main window.
Glide (Grid-based LIgand Docking with Energetics) searches for favorable interactions between one or more typically small ligand molecules and a typically larger receptor molecule, usually a protein. The shape and properties of the receptor are represented on a grid by several different sets of fields that provide progressively more accurate scoring of the ligand poses. The options in each tab of the panel allow you to define the receptor structure by excluding any cocrystallized ligand that may be present, determine the position and size of the active site as it will be represented by receptor grids, and set up Glide constraints. Ligand docking jobs cannot be performed until receptor grids have been generated.
Receptor grid generation requires a "prepared" structure: an all-atom structure with appropriate bond orders and formal charges. In most cases, the preparation process can be performed automatically using the Protein Preparation Wizard.
With the prepared structure in the Workspace, use the Receptor Grid Generation panel to set up the receptor grid generation job. When you have completed your setup, you can click the Settings button in the lower left corner of the panel to open the Receptor Grid Generation - Job settings dialog box.
As well as making standard job settings, you can set the directory in which to
save the grid files, by using the Directory for grid
files text box and Browse button. By default,
grid files are written to the current working directory. They are copied back
to this location from a temporary directory if the job is run on a remote
host. There are some restrictions on specifying the directory
for grid files: the directory cannot be a relative directory of the form
../mydir, and the job must be run on the local host.
The Output section also contains a Compress option, which can be used to compress the
grid-related files into a .zip archive.
Alternatively, you can choose Write from the Settings button menu to write the input files without starting the job. The files are written to the jobname subdirectory, where jobname is the name of the job that you specify. Any settings from the Job Settings dialog box are used to write the files.
To restore the default settings in all tabs, choose Reset Panel from the Settings button menu.
The Receptor Grid Generation panel contains five tabs, which are described in full in separate topics:
Receptor tab— Use this tab to define the receptor (by identifying the Workspace ligand, if one is present) and optionally to scale the van der Waals radii of receptor atoms.
Site tab— Use this tab to determine the position and size of the volume for which grids will be generated, representing the active site of the receptor.
Constraints tab— Use this tab to designate certain receptor atoms (positional/NOE, H-bond/metal constraints) for ligand-receptor interactions that you can then choose to require during docking jobs.
Rotatable Groups — Use this tab to specify groups that should be treated as rotatable in the grid generation. These groups are currently restricted to hydroxyls in Ser, Thr, and Tyr, and thiols in Cys.
Excluded Volumes— Use this tab to set up regions of space in which the ligand is penalized during docking.
The Job toolbar is used to make settings for a job and to start it.
Enter a name for the job in this text box.
This button opens the Job Settings dialog box. The arrow to the right opens a menu, from which you can make settings or perform actions that are related to the job.
The menu items are described below.
This icon indicates when there are jobs running for the application that belong to the current project. It starts spinning when the first job starts, and stops when there are no more jobs running. If a job fails to start, it changes to an exclamation point.
Clicking the button shows a small job status window that lists the job name and status for all active jobs submitted from the current panel (for Jaguar and MacroModel this means all jobs from any of the application panels). You can double-click on a row to open the Monitor panel and monitor the job, or click the Monitor button to open the Monitor panel and close the job status window. The job status is updated while the window is open. If a job finishes while the window is open, the job remains displayed but with the new status. The rows are colored according to the status: yellow for submitted, green for launched, running, or finished, red for incorporated, died, or killed. Click anywhere outside the window to close it.
Run the job with the current job settings.
The status bar displays information about the current job settings for the panel. This includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. It also displays a message for a short time when you start a new job.
The status bar also contains the Help button, which opens the help topic for the panel.
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