MacroModel Quick Start Guide - ISP

Chapter 2: Using Maestro6. Click on the aryl C–C bonds that need to be converted to double bonds.7. Click on the carbonyl C–O bond.8. Click the Increment formal charge button on the Build toolbar.9. Click on the nitrogen atom of the piperidine in the Workspace.The formal charge of the nitrogen atom is now +1, and the atom type is automaticallyadjusted. To check the formal charge, choose Formal Charge from the Label atoms buttonmenu. Choose Delete Labels from the Label atoms button menu to remove the label.Maestro also provides a tool for automatic assignment of bond orders. To use it, choose AssignBond Orders from the Tools menu. Automatic assignments should always be checked, becausethe rules that are used for the assignments cannot cover every possibility.2.7 Adding Hydrogens to a United Atom StructureModern force fields use all-atom structures, and Maestro contains a facility to rationally addthe appropriate number of hydrogens to carbon atoms with approximately the correct geometry.This exercise demonstrates how to use the tools in the Hydrogen Treatment panel to addhydrogens to the structure in the Workspace.1. From the Edit menu, choose Hydrogen Treatment.2. Choose All-atom with No-Lp from the Treatments option menu (see Figure 2.5).3. Under Modify hydrogen treatment, click All to add a full complement of hydrogens to theoriginal structure.4. Close the Hydrogen Treatment panel.You can also add hydrogen atoms with the Add hydrogens toolbar button. This button appliesthe current hydrogen treatment to the selected atoms.Now save the modified structure as a new entry in the project:1. Click the Create entry from Workspace button in the toolbar.14MacroModel 9.7 Quick Start Guide