Minimizing Structures

minimize, minimization, CTRL+M, Ctrl-M

To perform a quick minimization of a structure or part of a structure in the Workspace, you can do one of the following.

• All atoms:

  • Press Ctrl+M (⌘M) with no atoms selected
  • Edit → Minimize → All Atoms to minimize the entire Workspace

• Selected atoms:

  • Press Ctrl+M (⌘M)
  • Click Minimize Selected Atoms on the Favorites toolbar
  • Click the Minimize button in the 3D Builder panel
    
    
  • Edit → Minimize → Selected Atoms

• Ligand:

  • Press Ctrl+Shift+M (⇧⌘M)
  • Edit → Minimize → Ligand

• Binding Site + Ligand:

  • Press Ctrl+B (⌘B)
  • Edit → Minimize → Binding Sites + Ligands

This action performs a simple force-field minimization of the energy with the OPLS4 or OPLS_2005 force field. The minimization stops when the maximum change in distance between atoms is less than 0.1 Å, or 75 iterations have been performed. If you select atoms for minimization, the atoms bonded to the selection are included but constrained (150 kJ/mol force constant). Other atoms are kept frozen, but will influence the minimization by their interactions with the selected atoms.

Note: Entries in the Workspace that are locked are not minimized, and they are ignored when performing a minimization.

To cancel the minimization while it is running, and revert to the original structure, press Esc.

There are several other methods for minimizing a structure, depending on the type of structure and conditions:

• For more control over the parameters of a force-field minimization, including use of solvation, you can use MacroModel: click the Tasks button and browse to MacroModel → Minimization. See MacroModel — Minimization Panel for details. You can minimize multiple structures using this panel.

• To minimize a set of ligand-receptor complexes with optional constraints, you can use the MacroModel Embrace Minimization method: click the Tasks button and browse to MacroModel → Embrace Minimization. See Embrace Minimization Panel for details.

• To minimize a protein or parts of it, with optional periodic boundary conditions, implicit solvent, or implicit membrane, you can use Prime: click the Tasks button and browse to Protein Preparation and Refinement → Minimize. See Prime — Minimize Panel for details.

• To minimize several parts of a protein as rigid bodies, with optional periodic boundary conditions, implicit solvent, or implicit membrane, you can use Prime: click the Tasks button and browse to Protein Preparation and Refinement → Minimize as Rigid Body. See Minimize as Rigid Body Panel for details.

• To minimize a system for molecular dynamics that can include solute, solvent, protein, membrane, with periodic boundary conditions, you can use the Desmond Minimization panel, after setting up a model system in the System Builder Panel: click the Tasks button and browse to Desmond → Minimization. See Desmond — Minimization Panel for details.

• To minimize small-to-medium molecules with ab initio quantum-mechanics, you can use Jaguar. Choose one of the following:

  • Click the Tasks button and browse to General Modeling → Ab Initio QM
  • Click the Tasks button and browse to Quantum Mechanics → Optimization
  • Click the Tasks button and browse to Jaguar → Optimization
  • Click the Tasks button and browse to Materials → Quantum Mechanics → Molecular Quantum Mechanics → Optimization
  • Click the Tasks button and browse to Materials → Quantum Mechanics → Molecular Quantum Mechanics → More Molecular QM Tasks → Optimization

  See Jaguar - Optimization Panel for details.

• For a semiempirical QM minimization: click the Tasks button and browse to Quantum Mechanics → Semiempirical and ensure that Optimize geometry is selected. See Semiempirical Module Panel for details.

• For a QM/MM minimization of a large system such as a protein-ligand complex: click the Tasks button and browse to General Modeling → QM-MM and make MM minimization or QM optimization settings, or both. See QSite Panel for details.