MacroModel Quick Start Guide - ISP

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Chapter 3: Energy Calculation and Minimization3.2.2 Comparing Structural Results by SuperpositionOne useful way of comparing structural results is to superimpose them. Maestro provides toolsfor superimposing molecules based on a selection of atoms. For a pair of molecules, you canselect the corresponding atoms manually, and Maestro superimposes them by minimizing theRMSD of the selected atom distances. You can also select atoms in one structure using theAtom Selection dialog box or ASL and use this set as the basis of superposition. The atomspecification is applied to each entry included in the Workspace. This is useful for groups ofconformers, but may have unintended results for non-conformers. Superposition is discussedin detail in Section 9.3 of the Maestro User Manual. The following exercise demonstratessuperposition for two conformers.1. Click the Clear Workspace button on the toolbar.2. Open the Project Table panel (Open/Close project table toolbar button, choose ShowTable from the Project menu, or type CTRL+T).3. Click the In column for the unminimized job input structure.4. Control-click the In column for the minimized output structure.5. Click the Tile entries button in the main window toolbar.A dialog box is displayed warning that the coordinates of the entries may change. ClickYes to proceed.6. Choose Superposition from the Tools option menu.The Superposition panel opens.7. Click on the ASL tab.8. In the Superimpose by ASL text box, enter the expression not atom.element H andpress RETURN. (see Figure 3.5).The minimized structure is superimposed on the input structure, using only the nonhydrogen(heavy) atoms.9. Close the Superposition panel.34MacroModel 9.7 Quick Start Guide
Chapter 3: Energy Calculation and MinimizationFigure 3.5. The Superposition panel.3.2.3 Energy Minimization of Multiple StructuresA collection of structures, either conformers or non-conformers, can be minimized in onecomputation using the Multiple Minimization panel.1. Click the Import structures button on the main toolbar.The Import panel opens.1. Click Options.The Import Options dialog box opens.2. Ensure that Import all structures is selected, and click Close.The Import Options dialog box closes.MacroModel 9.7 Quick Start Guide 35
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