MacroModel Quick Start Guide - ISP

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Chapter 5: Other CalculationsFigure 5.6. The Multiple Minimization panel showing the Mult tab.5. In the Mini tab, enter 5000 in the Maximum iterations text box and enter 0.02 in the Convergencethreshold text box.6. In the Mult tab, select LogP estimation and choose Water from the Secondary solventoption menu (see Figure 5.6).7. Click Start to open the Start dialog box.8. Choose Append new entries as a new group from the Incorporate option menu.9. Enter logP in the Name text box.10. Click Start to launch the job.The Monitor panel is displayed. When the job is finished, the logP(o/w) value is displayedin the monitoring window.60MacroModel 9.7 Quick Start Guide
Chapter 5: Other Calculations5.6 Analysis of Molecular Structure With XClusterXCluster is a powerful structural clustering tool that uses molecular similarity as the clusteringcriterion. XCluster can be run from Maestro, using a set of conformers contained in the ProjectFacility as input and comparison data selected with Maestro’s picking tools. The calculationsare run and the results visualized with the XCluster interface, which is automatically started byMaestro.Note:This exercise cannot be performed under Windows.1. Import the structures from XCluster.mae from your working directory.The structures are imported as an entry group named XCluster, and are selected in theProject Table.2. Choose XCluster from the Applications menu.3. Choose Project Table (selected entries) from the Use structures from option menu (seeFigure 5.7).4. Under Cluster by, select Torsional RMS.5. Under Define comparison torsions, choose Atoms from the Pick menu and select atoms inthe Workspace for the torsions you want to examine, such as 2-1-14-15.Figure 5.7. The XCluster panel.MacroModel 9.7 Quick Start Guide 61
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MacroModel Quick Start Guide - ISP

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