MacroModel Quick Start Guide - ISP

Chapter 3: Energy Calculation and Minimization9. Under Incorporate, select Replace existing entries.10. In the Name text box, type MultMini.11. Click Start to launch the job.This job uses the selected entries as the input structure file and replaces the input entries in theProject Table with the resulting energy minimized structures at the conclusion of the job.For multi-conformer computations, you can eliminate duplicate minima and reduce the outputby using the tools in the Mult tab of the Multiple Minimization panel to define an energeticwindow and identify comparison atoms.3.2.4 Energy Minimization of a SubstructureThe time required to minimize large structures can be drastically reduced by focusing on aparticularly important section of the structure and restraining, freezing, or ignoring the rest.This exercise uses the protein-ligand complex from Section 2.1 to perform a substructure minimization.The ligand and all residues within 5.0 Å of the ligand are freely minimized. Theatoms between 5.0 Å and 10.0 Å from the ligand are restrained, while the atoms between10.0 Å and 15.0 Å from the ligand are frozen. The remaining atoms are ignored. For moreinformation on the Substructure facility, see Section 4.3.3 of the MacroModel User Manual.1. Click the Clear Workspace button on the toolbar.2. Import the structure in SubsMini.mae from your working directory.The ligand in this complex is molecule number 4.First, you will create an atom set for use in the definition of the substructures:1. From the Tools menu, choose Sets.The Sets panel opens.2. Click New (in the lower portion of the panel).3. Enter lig+5A in the Set name text box, and click OK.A new set is created, named lig+5A.4. In the Sets panel, under Atoms for set, select Show Markers.5. Choose Molecules from the Pick menu.6. In the Workspace, select an atom in the ligand.If you need to identify the ligand, color the atoms by molecule number, or use the FindAtoms panel described in Section 2.3 on page 9. If you do use Find Atoms, deselect Markfound atoms once you have selected the desired atom.MacroModel 9.7 Quick Start Guide 37