MacroModel Quick Start Guide - ISP

Chapter 4: Conformational SearchesThe moving, fixed, and frozen regions have now been defined and are indicated in the Workspaceas white, orange, and purple regions.To set up the search method and search variables:In this example, you will use the automatic setup features to define the MCMM conformationalsearch variables. You can set up variables either for the entire moving region (the substructure)or only for the ligand molecule. Atoms in the fixed or frozen atom regions do not have conformationalsearch variables assigned to them when using Perform Automatic Setup.8. In the CSearch tab, choose Torsional sampling (MCMM) from the Method menu.9. Ensure that Multi-ligand is not selected.10. Do one of the following:• Select Perform Automatic Setup during calculation to assign MCMM parameters forthe freely-moving substructure region automatically during the calculation.• Deselect Perform Automatic Setup during calculation, click Reset All Variables, thenclick Perform Automatic Setup to assign MCMM parameters to the entire freelymovingregion.• Enter the following command in the command input area of the main window toassign MCMM parameters to the ligand only:autosetup mol.n 411. For a shorter computation, change the value in the Number of steps text box to 200.To enter the job information and start the job:1. Click Start.2. In the Start dialog box, choose Append new entries as a new group from the Incorporateoption menu.3. Enter SubsAuto in the Name text box.4. Click Start to launch the job.The sample files included in the distribution have conformational search variables defined onlyfor the ligand.MacroModel 9.7 Quick Start Guide 49