Rapid Torsion Scan Panel

This panel enables you to scan the orientations around a ligand bond and see a breakdown of the energy for each orientation or state. The structure can be minimized at each scan angle during the scan, with constraints.

To open this panel, do one of the following:

  • In the Maestro main window, choose Edit → Rapid Torsion Scan
  • Click the Tasks button and browse to Workspace Operations → Rapid Torsion Scan
  • Click the Tasks button and browse to Materials → Classical Mechanics → Molecular Mechanics → Rapid Torsion Scan
  • Features
  • Additional Resources

Rapid Torsion Scan Panel Features

The picking and associated features (minimization, settings, increment, update) are not present when the panel is opened from the Workspace shortcut menu.

Pick torsion bond option

Select this option and pick an atom in the Workspace to define the bond to rotate around. The atom should be on the end of the bond that is rotated. The bond is scanned once it is picked, and the results presented in the table. The bond is marked with magenta markers.

Not present when the panel is opened from the Workspace shortcut menu.

Pick 4 atoms of dihedral option

Select this option and pick four atoms to define the dihedral for the scan. The second and third define the bond around which the rotation is done; the fourth defines the end that is rotated (it is in the rotated group). The bond is scanned once the dihedral is picked, and the results presented in the table. The four atoms of the dihedral are marked with magenta markers.

Not present when the panel is opened from the Workspace shortcut menu.

Include quick minimization option

Include a quick force-field minimization at each point along the scan, with the dihedral angle restrained to the specified value. This may result in a delay between picking and the population of the table. This minimization does not include the input structure. To make settings for the solvent and for fixing atoms (such as the core atoms), click the Settings link.

Not present when the panel is opened from the Workspace shortcut menu.

Settings link

Opens a pane in which you can make settings for the minimization. Not available if Include quick minimization is not selected.

Solvent option menu

Choose a solvent for the minimization, from Vacuum, Chloroform, Water, or Octanol.

Set fixed region option

Select atoms to fix using one of the options below.

Automatic option

All the atoms on one side of the defined dihedral are fixed. Whichever side has more atoms is picked.

Selected atoms option

Fix the selected atoms. You must select the atoms in the Workspace before updating the table.

SMARTS text box and Get from Selection button

Enter the SMARTS pattern for the atoms to fix in the text box, or select the atoms in the Workspace for the SMARTS pattern and click Get from Selection. When you click the button, a SMARTS pattern is generated for the Workspace selection and replaces the contents of the SMARTS text box. You can modify the SMARTS pattern after it is obtained from the Workspace.

Angle increment option menu

Choose the angle increment for the scan. The allowed increments are integer divisors of 180° in 30° increments. The default is 30°.

Not present when the panel is opened from the Workspace shortcut menu.

Update Table button

Recalculate the energies along the torsional coordinate and update the table. If you change the angle increment or the minimization settings, click this button to recalculate the energies with the new values.

Not present when the panel is opened from the Workspace shortcut menu.

Scanned object text

Displays the identity of the torsion. If you chose to pick a ligand torsion, the information gives two atom numbers and the direction to the rotated group; if you chose dihedral, the information gives four atom numbers, the last of which is in the rotated group.

Rotamer states table

Lists the rotamer states for the ligand bond with their computed energy contributions, in kcal/mol. Lower values indicate more stable rotamers. The columns can be sorted by clicking in the column header. The arrow displayed in the header shows the direction of the sort. The first row contains the original state. Select a row to display the rotamer in the Workspace.

Check boxes Check the box for a rotamer to select it for addition to the project.
# State number. The original state is labeled "original".
vdW+internal Sum of van der Waals and internal energies.
electrostatic Electrostatic energy.
Total Total energy, which is the sum of the contributions in the other columns.
Angle Dihedral angle value for the rotamer state, in degrees.
WaterMap WaterMap hydration site displacement contribution to the total energy. Added to the total if there is a water map in the Workspace.
Next and Previous buttons

Select the next or previous rotamer state in the table.

Select Lowest Energy button

This button selects the rotamer in the table that has the lowest total energy, excluding the original rotamer.

Restore Original State button

Restore the structure to the original rotamer state.

Reset button

Reset the panel to its default (clear all information).

Add Structures to Project button

Add the structures that are checked in the rotamers table to the project as new entries. The entries are placed in an entry group with a group title that identifies the bond scanned. Energy properties from the minimization are added as properties.

NOTE: The Add Structures to Project button is only enabled when rotamers are selected.
Plot Energy by Angle button

Open the Plot Coordinate Scan Results Panel to display an interactive plot of the energy against the torsional coordinate. Clicking on a plot point displays the structure in the Workspace with the torsion marked.

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