MacroModel Quick Start Guide - ISP

Chapter 4: Conformational Searches1. Redisplay all atoms by double-clicking the Display only selected atoms toolbar button.2. In the Substructure tab of the CSearch panel, clear any previously defined substructuresand shells.3. In the Freely moving atoms (substructure) section, enter the following in the ASL textbox:mol.n 44. Click New in the Shells (constrained and frozen atoms) section.5. Select Complete residues and enter 6.0 in the Radius text box.6. Select Freeze atoms.Maestro colors the frozen atoms orange; the remainder are ignored in the computation.7. Click Start.8. In the Start dialog box, choose Append new entries as a new group from the Incorporateoption menu.9. Enter LigandMCMM in the Name text box.10. Click Start to launch the job.This computation will take one to three hours, depending on your computer. When thecalculation is complete, the output structures are incorporated as a group namedLigandMCMM.11. Use the ePlayer to view the different low-energy orientations.For more information on the ePlayer, see Section 8.6 of the Maestro User Manual.4.5 Substructure Conformational Search withAutomatic SetupThe last exercise demonstrated a computation in which the ligand was manually assignedMonte Carlo conformational search parameters while the entire receptor was held frozen. Thisexercise demonstrates a modified conformational search that enables increased receptor flexibility,using Perform Automatic Setup to define the MCMM search variables.The steps below prepare a substructure conformational search calculation in which the receptoris divided into freely moving, fixed, and frozen regions. Computations using substructures useMacroModel 9.7 Quick Start Guide 47