Minimize as Rigid Body Panel

Minimize the energy of part of a protein by treating it as a rigid body and adjusting its location and orientation. The minimization can include freely moving atoms and multiple rigid bodies. The rest of the protein is frozen. The minimization can be run with periodic boundary conditions, in implicit solvent, and with an implicit membrane.

To open this panel, click the Tasks button and browse to Protein Preparation and Refinement → Minimize as Rigid Body.

  • Using
  • Features
  • Additional Resources

Using the Minimize as Rigid Body Panel

Rigid body minimization allows you to treat part of a system as a rigid body or a set of rigid bodies, with optional freely moving atoms, and freeze the rest of the system. The panel offers two standard selections of the rigid body, Protein and Ligand, and a Custom feature that allows you to choose the rigid body or bodies.

Rigid-body minimization is naturally a lot faster than a full minimization, so it is useful for obtaining results where the full optimization is too time-consuming, or to get a good starting position for a fuller refinement. It is often used in the early stages of X-ray refinement of a protein structure, for example. Below are some scenarios where rigid-body minimization might be useful.

  • Move a ligand into position in a receptor site, with the possibility of treating the side chains of the receptor flexibly.

  • Minimize the orientation of all side chains in a protein simultaneously.

  • Move a hinged protein into the open or closed conformation rigidly.

  • Refine the structure of a dimer resulting from protein-protein docking, with constraints to keep the protein in place, and flexible residues at the interface.

To set up a rigid-body minimization:

  1. Select an option for the part of the structure to minimize as a rigid body.

    The options are Protein, Ligand, and Custom. The protein and the ligand are automatically detected. If you select Custom, the Atoms for rigid-body minimization picking tools are displayed, so you can specify the rigid parts of the structure.

  2. If you selected Custom, pick the atoms to use for the rigid body using the Atoms for rigid-body minimization standard picking tools.

    The atoms that you choose do not have to be connected: if they are not, each connected piece is treated as a rigid body. For example, if you choose Protein Side Chains from the Atom Selections button menu, each side chain is treated as a rigid body.

  3. Select Include freely moving atoms if you want to add atoms that are minimized without being constrained to a rigid body.

    When you select this option, the Atoms for free minimization picking tools are displayed below the option.

  4. If you selected the option to include freely moving atoms, select the desired atoms using the Atoms for free minimization standard picking tools.

    These atoms are minimized individually along with the rigid body. You might, for example, pick atoms on the boundary between the rigid body and the rest of the structure for free minimization. The atom selection should not contain any atoms that are part of the rigid body region: if it does, they are removed from the freely moving selection.

  5. (Optional) Click Constraints to set up any additional constraints on the structures.

    You might, for example, apply a distance constraint between two rigid proteins, to prevent them from drifting apart rather than moving closer together.

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 prime Command Help and prime—Build and Refine Protein Structures.

Minimize as Rigid Body Panel Features

Use structures from option menu

Choose the structure source for the current task.

  • Project Table (selected entries)—Use the entries that are currently selected in the Project Table.
  • Workspace (included entry)—Use the entry that is currently included in the Workspace. Only one entry must be included in the Workspace.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
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 model option menu

Choose a continuum solvation model for the refinement. The choices are:

  • VSGB—Use the variable-dielectric generalized Born model, which incorporates residue-dependent effects. The solvent is water.
  • Vacuum—Do not include solvation.
  • Chloroform—Use chloroform as the solvent, modeled with the Surface Generalized Born (SGB) method.
Force field option menu

Choose the force field for the current task. The choices are OPLS_2005 and OPLS4. The default is OPLS4 if it is available, otherwise it is OPLS_2005, unless you set the default in the Force Field settings section of the Preferences Panel.

Use customized version option

Use your customized version of the OPLS4 force field, rather than the standard version in the distribution. Only available when you choose OPLS4 from the Force field option menu and you have the appropriate license. This option is set by default to the value of the Use custom parameters by default option in the Preferences panel, under Jobs - Force field, when the current panel is opened. The default directory for the customized version can also be specified as a preference, in the same location.

If the customized version is missing or invalid, the text of this option turns orange and an orange warning icon is displayed to the right, with a tooltip about the problem.

Parameter set button

Select the set of custom parameters for the OPLS4 force field. Opens the Set Custom Parameters Location Dialog Box. Only available when you choose OPLS4 from the Force field option menu and you have the appropriate license.

Minimize as rigid body options

Select an option for the part of the structure to minimize as a rigid body, from Protein, Ligand, and Custom. If you select Custom, the Atoms for rigid-body minimization picking tools are displayed, so you can specify the rigid parts of the structure.

Atoms for rigid-body minimization picking tools

Pick the atoms to use for the rigid body using the standard picking tools. The atoms that you choose do not have to be connected: if they are not, each connected piece is treated as a rigid body. For example, if you choose Protein Side Chains from the Atom Selections button menu, each side chain is treated as a rigid body.

Include freely moving atoms option

Select atoms that are minimized without constraints. When you select this option, the Atoms for free minimization picking tools are displayed below the option.

Atoms for free minimization picking tools

Select atoms for free minimization using the standard picking tools. These atoms are minimized without any constraints, along with the rigid body. You might, for example, want to pick atoms on the boundary between the rigid body and the rest of the structure for free minimization. The atom selection should not contain any atoms that are part of the rigid body region: if it does, they are removed from the freely moving selection.

Constraints button

Open the Minimize as Rigid Body - Constraints Dialog Box, to set up distance (atom-pair) and Cartesian (initial position) constraints. This can be useful to ensure that the rigid body does not drift too far from the frozen part of the protein, or to constrain the system to a particular configuration.

Options button

Open the Minimize as Rigid Body - Options Dialog Box to set up options, including use of an implicit membrane and crystal symmetry, the solvent dielectric constant, algorithm selection, and convergence criteria.

Job toolbar

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

The Job Settings button opens the Minimize as Rigid Body - 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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