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Ligand Docking Panel |
The Glide Ligand Docking panel is used to set up and run docking jobs using previously calculated receptor grids. To generate receptor grids, see the Receptor Grid Generation Panel topic.
To open the Ligand Docking panel, you can:
Choose Applications → Glide → Ligand Docking in the main window.
Choose Tasks → Docking → Glide Docking in the main window.
Glide ligand docking jobs require a set of previously calculated receptor grids and one or more ligand structures. Preparation of the ligands before docking is strongly recommended. LigPrep or MacroModel can be used to prepare ligands. If a correct Lewis structure cannot be generated for a ligand, it will be skipped by the docking job.
When you have chosen settings for the options in the tabs, you can choose Job Settings from the Settings button in the lower left corner of the panel.
This opens the Ligand Docking - Job Settings dialog box. Along with the standard controls, this dialog box includes controls for distributed processing: options and text boxes for specifying the number of subjobs or the maximum number of ligands per subjob, and a table of hosts, in which you can select hosts and specify the number of processors to use on each. For details, see the Job Settings Dialog Box topic. The number of subjobs cannot be set to fewer than the number of processors: if you specify more processors, the number of subjobs is adjusted upward to match. The ligands are divided evenly between the subjobs when the job is run.
You can also incorporate the docking results into the project by choosing from the Incorporate option menu; however, incorporating a large number of ligands can take a long time.
Default values are used for all other command-line options. For example, the range of ligands that is divided into subjobs is the entire range of ligands to dock as specified in the Range text boxes in the Ligands tab. If you are using the default range (dock all ligands in the file), glide creates j subjobs starting with the first ligand in the file and ending with the last. If you have specified multiple files, all ligands in all files are distributed among the subjobs. To use different settings for this and other options, run glide from the command line, as described in the Glide User Manual.
If the grid files are not available on the host from which you submit the job, the job will not be submitted, as a check is done to confirm the availability of the grid. If you want to submit a job with a grid that is not available on the local host, you can do so from the command line.
Alternatively, you can choose Write from the Settings button menu to write the input files without starting the job. In addition to the input file, a shell script is written that you can use to run the job. The script is written with the current settings from the Job Settings dialog box. The files are written to a subdirectory in the current directory. Both the subdirectory and the files are named using the job name.
To restore the default settings in all tabs, choose Reset Panel from the Settings button menu.
The main part of the Ligand Docking panel contains several tabs, which are described in separate topics, linked below. The remaining features are described in this topic.
Click Browse to open a file selector and choose
a grid for your docking job to use. The grid files are stored in compressed
form, in a .zip file. The file name is displayed in
the Receptor grid text box. You can also enter the
file name directly into the text box. The grid file must be accessible to the
host on which you are running Maestro.
If you plan to use SP-Peptide docking, you must select a grid that was generated for this docking mode (with Generate grid suitable for peptide docking selected in the Receptor tab of the Receptor Grid Generation panel). If you plan to use any of the other three docking modes, you must not select a grid generated for SP-Peptide docking.
If you want to use grids from earlier releases in which the grid was not compressed, you can also choose the .grd file for the grid to use that grid.
Display the receptor in the Workspace.
Display the outer (purple) and inner (green) grid boxes in the Workspace, and the grid center. These are the boxes that are displayed when you set up the grid calculation. The box parameters are stored in the Maestro file for the receptor. (Grid boxes cannot displayed for grids generated with software prior to Suite 2012.)
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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