MacroModel Quick Start Guide - ISP

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Chapter 4: Conformational SearchesFigure 4.1. The Conformational Search panel showing the CSearch tab.12. Click Start to launch the job.This calculation takes a couple of minutes to finish. The Workspace is updated with thecurrent low-energy structure during the calculation.The output structure file, MCMM-out.mae, contains all structures found within the specifiedenergetic window. The output log file, MCMM.log, includes a convenient listing of the molecularmechanics potential energy of all the output structures.4.2 Serial MCMM Conformational SearchSerial MCMM conformational searches perform an MCMM conformation search on eachinput structure, with MCMM parameters that are set up automatically (by means of an AUTOopcode in the command file).42MacroModel 9.7 Quick Start Guide
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
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MacroModel Quick Start Guide - ISP

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