MacroModel Quick Start Guide - ISP

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Chapter 5: Other CalculationsFigure 5.1. The Embrace Minimization panel showing the Embrace tab.3. Choose Applications > MacroModel > Embrace Minimization from the main window.4. In the Potential tab, choose OPLS_2001 from the Force field option menu and chooseNone from the Solvent option menu.5. In the Mini tab, enter 1000 in the Maximum Iterations text box.6. Click the Embrace tab (see Figure 5.1).7. Under Source of ligands, select Selected entries.8. Under Receptor, select First selected entry.9. Under Association energy mode, select Interaction energy mode.10. Under Structures saved, select Complexes only.52MacroModel 9.7 Quick Start Guide
Chapter 5: Other Calculations11. In the Substructure tab, click the Read .sbc file button in the lower right corner of thepanel and select Embrace.sbc from your working directory.The atoms in the structure are highlighted: white markers for the substructure, orangemarkers for shell 1, and purple markers for shell 2.12. Click Start to open the Start dialog box.13. Choose Append new entries from the Incorporate option menu.14. Enter Embrace in the Name text box.15. Click Start to launch the job.This calculation may take 10 minutes. When the calculation is complete, the results are placedin a table at the end of the Embrace.log file and are incorporated into the Project Table.5.2 Molecular DynamicsMolecular dynamics calculations simulate molecular movement over time using Newton’sequations of motion. In this exercise, you will run an MC/SD dynamics calculation.In the MC/SD simulation, an initial minimization is performed to ensure that the structure is ata minimum on the potential energy surface. Geometric structural parameters can be monitoredover the course of the dynamics simulation, and structures can be sampled during the simulationat constant intervals. Since MC/SD uses Monte Carlo methods, it is also necessary todefine the Monte Carlo parameters.1. Import the structure in MCSD.mae from your working directory.This structure has been minimized to a low gradient with MMFFs in the gas phase.2. Choose Applications > MacroModel > MC/SD from the main window.3. Choose Workspace (included entry) from the Use structures from option menu.4. In the Potential tab, choose MMFFs from the Force field option menu and choose Nonefrom the Solvent option menu.5. In the Constraints tab, clear any previously set constraints by clicking the Reset All buttonin both the Constrain section and the Freeze section.6. In the Substructure tab, click the Clear button in both the Atoms for substructure sectionand in the Shells section, to clear any previously defined substructures and shells.7. In the Shells section, click Delete Shells until all shells are deleted.MacroModel 9.7 Quick Start Guide 53
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MacroModel Quick Start Guide - ISP

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