MacroModel Quick Start Guide - ISP

Chapter 3: Energy Calculation and MinimizationFigure 3.3. The Stretch panel.3.1.2 Investigating Force Field Interactions1. From the Tools menu, choose Force Field Viewer.2. Click Browse, select Ecalc-out.mmo from the Files list, and click Open.3. Click Stretch to open the Stretch panel (see Figure 3.3).4. Click on a numbered pair in the list on the left to select a stretching interaction and displayit in the Workspace with a magnifying glass icon.5. To sort the stretching interactions, select Sort by Energy in the lower center portion of thepanel.The list of stretching interactions is re-sorted so that the stretch with the lowest energy(that is, the least strained atom pair) is at the top of the list.6. To investigate a particular stretching interaction, choose Bond from the Define Stretchpick menu and click on the desired bond in the Workspace.7. To view stretching interactions by parameter quality, select the desired quality level fromthe Show option menu. View relevant force field parameters by clicking Show force field.This feature has limited utility for the BMFF force fields (MMFF and OPLS_2001).The other panels opened from the Force Field Viewer panel are similar to the Stretch panel.You can experiment with bond angle, electrostatic, and other parameters.8. When you have finished, close the Stretch panel and the Force Field Viewer.MacroModel 9.7 Quick Start Guide 31