MacroModel Quick Start Guide - ISP

Chapter 4: Conformational Searches1. Import Serial.mae from your working directory.2. In the Project Table, select the three imported entries.3. Choose Applications > MacroModel > Conformational Search from the main window.4. Choose Project Table (selected entries) from the Use structures from option menu.5. In the CSearch tab, choose Torsional sampling (MCMM) from the Method option menu.6. Select Multi-ligand.Perform automatic setup during calculation (at the top of the panel) is automaticallyselected and dimmed because it is mandatory for this type of calculation.7. Enter 100 in the Number of steps text box.8. Click Start to open the Start dialog box.9. Choose Append new entries as a new group from the Incorporate option menu.10. Enter SerialMCMM in the Name text box.11. Click Start to launch the job.The output structures are incorporated into the Project Table when the conformationalsearch is finished as a group named SerialMCMM.The serial_split utility can be used to divide the results of a serial search into individualoutput files for the individual input structures. See Section 18.7 of the MacroModel UserManual for more information.4.3 Serial Low-Mode SearchLow-mode searching explores the low-frequency eigenvectors of the system to generate newconformations. A low-mode calculation does not require the designation of ring structures andvariable torsion angles.1. Import Serial.mae from your working directory.2. In the Project Table, select the three imported entries.3. Choose Applications > MacroModel > Conformational Search from the main window.4. Choose Project Table (selected entries) from the Use structures from option menu.5. In the CSearch tab, choose Low-mode sampling from the Method option menu and selectMulti-ligand.6. Enter 100 in the Number of steps text box.MacroModel 9.7 Quick Start Guide 43