Refine Protein-Ligand Complex Panel

Refine the structure of protein-ligand complexes. The refinement can be restricted to the region around the ligand, and can sample positions and conformations of the ligand. The refinement 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 → Refine Protein-Ligand Complex.

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.

  • Features
  • Additional Resources

Refine Protein-Ligand Complex Panel Features

Use structures from option menu

Choose the structure source for the refinement.

  • 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.

The structure source supports the following cases:

  • The Workspace or the Project Table selection contains a receptor-ligand complex.
  • The Workspace or the Project Table selection contains a receptor in one entry and a single ligand structure in a second entry.
  • The Project Table selection or the file contains a set of receptor-ligand complexes with a single ligand in each.

If there are multiple ligands in any entry, you must pick the one you want to use, in the Workspace. Note that the structure must also be in the Workspace to set up constraints, pick custom atoms for refinement, or add a membrane.

The protein structures must be already prepared for calculations, preferably by using the Protein Preparation Workflow Panel.

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.

Pick ligand option

Pick a ligand atom in the Workspace to define the ligand. This is necessary if any of the entries containing the ligand has multiple ligands.

Refine atoms options

Select an option for the protein atoms to refine along with the ligand:

  • Within N Å of ligand—Refine the protein residues that have atoms within the specified distance of the ligand.
  • Entire protein—Refine all residues in the protein. This is likely to take some time.
  • Custom—Select the protein atoms to refine. When you select this option, the Protein atoms for refinement picking tools are displayed, so you can pick the atoms.
Protein atoms for refinement picking tools

Select the protein atoms to refine using the standard picking tools. Only available when you select Custom under Refine atoms.

Sampling algorithm option menu

Choose the algorithm used for sampling the part of the structure that is being refined:

  • Local optimization—Predict side chains and minimize the protein residues, then minimize the ligand and the protein atoms selected for refinement.

  • Minimization Monte Carlo—Perform a Monte Carlo sampling of the conformations of the refinement region. The sampling includes "inner" steps, in which only the short-range forces are updated, and outer steps, in which the long-range forces and solvent interaction is updated.

  • Hierarchical optimization—Systematically sample ligand positions, orientations, and conformations along with receptor residues. See Hierarchical Sampling Technical Details for more information.

Constraints button

Open the Constraints Dialog Box, to set up distance (atom-pair) and Cartesian (initial position) constraints.

Options button

Open the Options Dialog Box to set up options, including use of an implicit membrane and crystal symmetry, the solvent dielectric constant, and sampling options for the chosen sampling algorithm.

Job toolbar

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

The Job Settings button opens the Refine Protein-Ligand Complex - 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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