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Geometry Cleanup |
The Geometry Cleanup facility in Maestro performs a force-field minimization of the structure or of the selected atoms. Two minimizers are available: the built-in minimizer, which uses the OPLS_2005 force field, is faster and can handle larger structures, and the UFF (universal force field) minimizer, which is slower, but has a much wider range of atom types available. By default, the built-in minimizer is used, but you can choose the minimizer from the Clean up button menu (Built-in or UFF) or set a preference for the minimizer in the Builder – Geometry cleanup tab of the Preferences panel. The preferences and the button menu settings are linked.
The effect of the cleanup is to realign atoms that are too crowded and correct unphysical geometry that can occur when building molecules from the Builder. In general, it eliminates distortions that can cause jobs in MacroModel or Jaguar (for instance) to fail.
Minimization proceeds for 300 cycles or until the maximum atom displacement is less than 0.05 Å. By default, when using the built-in minimizer, atoms within 5 Å of the selected atoms are restrained with a moderate restraint, and atoms within 5 Å of these atoms are restrained with a much tighter restraint, while the rest of the atoms are frozen. You can set a preference to freeze all unselected atoms in the Builder - Geometry cleanup tab of the Preferences panel.
To clean up the geometry, you can:
Choose Edit → Build → Clean Up Geometry in the main window.
Press U in the main window.
Click the Clean up button on the Build toolbar in the main window.
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