One-Step Glide Docking Panel

Perform Glide docking with a limited set of options, running both the grid generation and the docking in the same job.

To open this panel: click the Tasks button and browse to Receptor-Based Virtual Screening → One-Step Ligand Docking.

To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write.

  • Features
  • Additional Resources

One-Step Glide Docking Panel Features

Dock ligands from option menu

Choose the structure source for docking.

  • Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries.
  • File—Use the specified file. When this option is selected, the Ligand file text box and Browse button are displayed.
Open Project Table button

Open the Project Table panel, so you can select the entries for the structure source.

Ligand file text box and Browse button

Enter the file name in this text box, or click Browse and navigate to the file. The name of the file you selected is displayed in the text box.

Dock to the Workspace receptor option

Dock ligands to the receptor that is displayed in the Workspace (for which a grid is generated). The following options can be used to define the receptor grid

Pick ligand option

If there is a ligand in the Workspace, you can pick it to define the center of the grid box, and also exclude it from the receptor.

Box center boxes

These boxes display the coordinates of the grid box center. You cannot change the values in these boxes. If there is no ligand in the Workspace, you will need to ensure that the receptor is positioned so the desired box center is at the origin.

Dock ligands with length <= option

Use this slider to choose an appropriate maximum ligand length (maximum atom-to-atom distance). This length determines the size of the grid box. The slider is set to 15 Å by default, but adjusts to the size of the Workspace ligand when it is picked.

Pick receptor H-bond constraint atoms

Select this option to pick receptor atoms for hydrogen-bond constraints. See the Constraints tab section in the Receptor Grid Generation Panel topic for more information.

Constraint atoms text box

List of atoms picked for hydrogen-bond constraints. These are given as atom numbers.

Dock to pregenerated grids option

Dock the ligands to a receptor for which you have an existing grid.

Grid file text box and Browse button

Specify the grid file for the receptor: enter the file name in the text box, or click Browse and navigate to the grid file.

Precision options

Choose a docking precision option:

HTVS (high throughput virtual screening)

High-throughput virtual screening (HTVS) docking is intended for the rapid screening of very large numbers of ligands. HTVS has much more restricted conformational sampling than SP docking, and cannot be used with score-in-place. Advanced settings are not available for HTVS, but are fixed at predetermined values.

SP (standard precision)

Standard-precision (SP) docking is appropriate for screening ligands of unknown quality in large numbers.

Docking method options

Choose a method for how the ligand is docked:

  • Flexible—Generates conformations internally during the docking process. Conformation generation is limited to variation around acyclic torsion bonds, sampling of low-energy ring conformations, and generation of pyramidalizations at certain trigonal nitrogen centers, e.g. in sulfonamides.
  • Rigid—Allows the existing ligand structure to be translated and rigidly rotated relative to the receptor, but skips the conformation generation step.
  • None (refine only)—Uses the input coordinates to perform an optimization of the ligand structure in the field of the receptor, and then the ligand is scored. For HTVS and SP, a minimization is performed; for XP, the ligand is regrown in place.
  • None (score in place)—Uses the input ligand coordinates to position the ligands for scoring. This option is useful to score the reference ligand in its cocrystallized or modeled position, or as a post-processing step on Glide-generated poses to obtain individual components of the GlideScore.
Write out at most n poses per ligand text box

Limit the number of poses per ligand written to the sorted pose file. The default choice of 1 pose per ligand is intended for database screening. A larger value may be appropriate for lead-optimization studies or whenever several "reasonable" poses are wanted, for example, to generate a variety of docked poses for study with a post-docking script or application.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the One-Step Glide Docking - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

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