Add Hydrogens - Advanced Panel

• Summary
• Opening the Add Hydrogens - Advanced Panel
• Using the Add Hydrogens - Advanced Panel
• Add Hydrogens - Advanced Panel Features

Summary

The Add Hydrogens - Advanced panel is used to delete or add hydrogens to be consistent with the currently selected hydrogen treatment. A "hydrogen treatment" in this context refers to a policy that determines which atoms are to have hydrogens or lone pairs attached. Several different treatments are supplied with Maestro. Each of these treatments is associated with a particular molecular mechanics force field. Note, however, that some treatments are suitable for several force fields.

Opening the Add Hydrogens - Advanced Panel

To open the Add Hydrogens - Advanced panel, you can:

• Choose Edit → Add Hydrogens → Advanced in the main window.

Using the Add Hydrogens - Advanced Panel

To change the current hydrogen treatment, select the desired treatment from the Treatment option menu. Descriptions of the treatments, including which force fields are compatible, appear in the Description text box when the treatments are selected. To apply the treatment, use the standard picking tools.

You can also apply the current hydrogen treatment using the Add H button on the Edit toolbar in the main window.

This button has a menu from which you can select a structural unit to pick for hydrogen treatment, or open the Atom Selection dialog box to select the atoms for hydrogen treatment.

Add Hydrogens - Advanced Panel Features

• Treatment option menu
• Description text box
• Modify Hydrogen Treatment picking controls

Treatment option menu

This option menu can be used to select a hydrogen treatment.

Description text box

This text box gives a brief synopsis of the currently selected treatment and includes information about which force fields the current treatment is suitable for.

Modify Hydrogen Treatment picking controls

The standard picking tools are used to select atoms that will have hydrogens or lone pairs added or deleted.

NOTE: HYDROGEN ADDITION OR DELETION ONLY TAKES PLACE TO BE CONSISTENT WITH THE CURRENT TREATMENT. For example, if the currently selected treatment calls for all atoms to have hydrogens and the current structure already has hydrogens on all atoms, then no action is taken.

Also note that the current hydrogen treatment changes automatically as the force field is changed using the controls in the Potential tab within any MacroModel panel. The treatment selected is one of those which is known to be acceptable for the newly selected force field.