MacroModel Quick Start Guide - ISP

MacroModel Quick Start GuideChapter 3Chapter 3:Energy Calculation and Minimization3.1 Current Energy CalculationsMany types of energetic calculations are available using MacroModel. This section introducesthe MacroModel energetic panels and basic energetic parameters. These exercises calculate thecurrent molecular mechanics energy of a structure in gas phase, then in solution phase.Before starting the calculations, import the substituted thymine structure from Ecalc.mae,which you copied to your working directory in Section 1.3 on page 2. If you have not copiedthese files, do so now. See Section 2.1 on page 5 for instructions on importing structures.3.1.1 Calculating the Gas-phase Potential Energy1. Choose MacroModel > Current Energy from the Applications menu2. Choose Workspace (included entry) from the Use structures from option menu.3. In the Potential tab, choose MMFFs from the Force Field option menu and choose Nonefrom the Solvent option menu.4. In the ECalc tab, choose Complete from the Energy Listing option menu.5. Click Start.The Start dialog box opens (see Figure 3.1).6. Choose Replace existing entries from the Incorporate option menu.7. Enter Ecalc in the Name text box.Figure 3.1. The Start dialog box.MacroModel 9.7 Quick Start Guide 29