MacroModel Quick Start Guide - ISP

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Chapter 5: Other CalculationsFigure 5.2. The MC/SD panel showing the MC/SD tab.8. In the Mini tab, enter 5000 in the Maximum iterations text box and enter 0.002 in the Convergencethreshold text box.These parameters are required for the initial minimization.9. In the Monitor tab, enter 10 in the Number of structures to sample text box.You can use the buttons in this tab if you want to conduct additional structuralmonitoring.10. In the Dynamics tab, choose Stochastic dynamics from the Method option menu, andchoose Nothing from the SHAKE option menu.SHAKE is not recommended for MC/SD simulations.11. In the MCSD tab, click Perform Automatic Setup (see Figure 5.2).To view the selected torsions, click Torsion Rotations in the middle of the panel.54MacroModel 9.7 Quick Start Guide
Chapter 5: Other Calculations12. Click Start to open the Start dialog box.13. Choose Append new entries as a new group from the Incorporate option menu.14. Enter MCSD in the Name text box.15. Click Start to launch the job.The ten sampled structures are incorporated into the Project Table at the completion ofthe computation.After incorporation, you can view the sample trajectory using Maestro’s ePlayer. The incorporatedstructures should already be selected in the Project Table. Click the Play forward button inthe Project Table toolbar to view the trajectory in the Workspace.For more information on the ePlayer, see Section 8.6 of the Maestro User Manual.5.3 Creating Energy Profiles From Coordinate ScansA contour diagram describing the molecular mechanics potential energy of a structure, relativeto the value of either one or two coordinates (distances, angles, or dihedrals), can be generatedwith MacroModel. These exercises demonstrate how to produce a contour diagram describingthe variation in energy of a molecule with respect to rotation of two dihedral angles.5.3.1 Performing a Coordinate Scan Calculation1. Import the structure in Ddrive.mae from your working directory.2. Choose Applications > MacroModel > Coordinate Scan from the main window.The Coordinate Scan panel opens.3. Choose Workspace (included entry) from the Use structures from option menu.4. In the Potential tab, choose MMFFs from the Force Field menu and choose None from theSolvent option menu.5. In the Substructure tab, click the Clear button to clear any substructure.6. Click Delete Shell enough times to clear all shells.MacroModel 9.7 Quick Start Guide 55
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