Strain Energy Calculation and Rescoring Panel

For each ligand pose in an input file, run a tightly constrained minimization and an unconstrained minimization with MacroModel. The energy difference is used to determine the strain penalty to add to the GlideScore. This panel offers more flexibility than the strain penalty calculated during Glide ligand docking.

To open this panel: click the Tasks button and browse to Receptor-Based Virtual Screening → Strain Energy Rescoring.

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. For information on command usage and options, see strain_rescore.py Command Help.

  • Features
  • Additional Resources

Strain Energy Calculation and Rescoring Panel Features

Use structures from option menu

Choose the structure source for the current task.

  • 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 File name 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.

File name 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.

Solvation option menu

Choose the solvation model for the calculations. The choices are Water, Vacuum (gas phase), and 4RDDD (4r distance-dependent dielectric).

Run conformation search to report global minima option

Run a MacroModel conformational search to find the global minimum in the unrestrained calculation. Otherwise a minimization is performed starting from the input geometry.

Energy offset options and text boxes

Specify the energy offset for the strain corrections. This value is subtracted from the calculated energy difference before the penalty is calculated.

  • Constant—Use the constant offset value given in the text box. The offset is the same for each ligand.
  • Per rotor—
Penalty scale factor text box

Scale the calculated energy difference between the "bound" and "free" states by the value in the text box to produce the GlideScore penalty.

Restraint type options and settings

Specify the type of restraints to apply for the restrained calculation, and set parameters for the restraints.

Use Cartesian restraints option

Use Cartesian restraints for the restrained minimization. The "free" minimization in this case uses a flat-bottomed potential with a half-width of 1.0 Å. The settings for this potential can be given with the options below.

Bound state half width text box

Specify the half-width for the Cartesian restraints in the "bound" (restrained) configuration, in angstroms.

Force constant text box

Specify the force constant for the Cartesian restraints, in kcal mol-1 Å-2.

Use torsional restraints option

Use torsional restraints for the restrained minimization. The settings for this potential can be given with the options below.

Bound state half-width text box

Specify the half-width for the torsional restraints in the "bound" (restrained) configuration, in degrees.

Force constant text box

Specify the force constant for the torsional restraints, in kcal mol-1 deg-2.

Job toolbar

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

The Job Settings button opens the Strain Energy Calculation and Rescoring - 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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