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Ligand Docking — Torsional Constraints Tab |
In this tab you can set up torsional constraints for all ligands. This is done by defining SMARTS patterns that are matched in the ligands, and sets of torsions that are constrained relative to those SMARTS patterns.
This tab is only available when either Dock flexibly or Refine is selected in the Settings tab. All constraints defined in this tab are applied during docking.
To set torsional constraints, first you must define a SMARTS pattern that matches the group on the ligands that you want to constrain (and does not match groups that you do not want to constrain), and then define the torsion or torsions within that SMARTS pattern whose values are to be constrained. You can define more than one group to constrain, and more than one torsion in each group. The basic procedure is:
Pick atoms in the Workspace ligand that define the group.
Click New.
The New Torsion Pattern dialog box opens.
Click From Workspace Selection.
The SMARTS pattern is entered into the text box.
Click OK.
The SMARTS pattern is added to the Patterns table and marked on the Workspace ligand.
Select an option for the torsions to constrain: All torsions, or Specified torsions.
If you chose Specified torsions, continue with the steps below.
Pick four atoms in the SMARTS pattern on the Workspace ligand to define a torsion for the pattern.
The atoms must be in adjacent bonds and not all in a ring. The torsion is added to the torsions table along with the current value of the torsional angle.
Choose whether to set the angle to a fixed value for all ligands or to fix the angle independently at the input value for each ligand. You set the angle to a fixed value by selecting the check box in the Set angle column of the table, and editing the Angle table cell to set the desired torsional angle.
This table lists the SMARTS patterns used to define the torsional constraints.
| SMARTS pattern | SMARTS pattern that is to be used for a constraint. |
| Atoms | Number of atoms in the SMARTS pattern |
| Torsions | Number of torsions that are defined for the SMARTS pattern. |
These buttons perform actions on the rows of the Patterns table.
Create a new SMARTS pattern in the table. Opens the New Torsion Pattern dialog box, in which you can type in a SMARTS pattern or get the SMARTS pattern from the current Workspace atom selection.
Delete the rows that are selected in the table.
Delete all rows in the table.
These options allow you to choose which torsions to constrain.
This table lists the torsions that have been selected for use as constraints for the pattern that is selected in the Patterns table.
| Atoms | List of atom indices in the SMARTS pattern that define the torsion. |
| Set Angle | Check boxes for setting the corresponding angles to the value specified in the Angle column for each ligand. |
| Angle | Angle to which the torsion should be constrained in all ligands. By default, the torsion is constrained for each ligand to the value it had when it was read by Glide. You can edit this table cell to change the angle. |
Select this option to pick torsions in the Workspace. Four atoms must be picked to define the torsion. The atom indices (as defined by the SMARTS pattern) are listed in the Atoms column of the torsions table when the fourth atom is picked, and the angle in the Workspace structure is shown in the Angle column.
These buttons perform actions on the rows of the torsions table.
Delete the rows that are selected in the table.
Delete all rows in the table.
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