MacroModel Quick Start Guide - ISP

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Chapter 3: Energy Calculation and Minimization9. Click the Clear Workspace button on the toolbar.3.1.3 Calculating the Solution-phase Current Energy1. Include the Ecalc entry in the Workspace.2. Choose MacroModel > Current Energy from the Applications menu.3. Choose Workspace (included entry) from the Use structures from option menu.4. In the Potential tab, choose MMFFs from the Force Field option menu, and choose Waterfrom the Solvent option menu.5. Enter 1.0 in the Dielectric constant text box.For all calculations using the GB/SA solvation model, the constant dielectric treatment isautomatically used for the electrostatic part of the calculation. We recommend using alow molecular dielectric constant (for example, 1.0).6. Click the ECalc tab and choose None from the Energy Listing option menu.7. Click Start to open the Start dialog box.8. Under Incorporate, select Append new entries as a new group.9. In the Name text box, type EcalcSolv.10. Click Start to launch the job.Because you selected the Append new entries option, when the job finishes, a new entry isadded to the Project Table with the total potential energy as a property. You can use the outputin the Monitor panel or in the output Ecalc.log and EcalcSolv.log files to examine thedetails of the energies for the gas-phase and solution-phase calculations.3.2 Energy MinimizationMacroModel energy minimizations are set up from the Minimization and Multiple Minimizationpanels within Maestro. Minimization calculations can be performed on single structures andmulti-structure collections. In addition, for single structure calculations, the MacroModelsubstructure facility can be used to select fixed and frozen atoms for the minimization of asubset of atoms within a large structure.For the next two exercises, you can either use the structure from Section 3.1.3 or importMini.mae from your working directory. The entry title is Ecalc. See Section 2.1 on page 5 forinstructions on importing structures.32MacroModel 9.7 Quick Start Guide
Chapter 3: Energy Calculation and MinimizationFigure 3.4. The Minimization panel showing the Mini tab.3.2.1 Energy Minimization of a Single Structure1. Choose MacroModel > Minimization from the Applications menu.2. Choose Workspace (included entry) from the Use structures from option menu.3. Click Start to open the Start dialog box.4. Under Incorporate, select Append new entries individually.5. In the Name text box, type Mini.6. Click Start to launch the job.The Monitor panel is displayed. An intermediate structure is displayed in the Workspace withthe atoms colored according to the energy gradient of the minimization at the time of monitoring.After job completion, the final minimized structure is incorporated into the project as anew entry. If you wish to change the default minimization setting, click the Mini tab.MacroModel 9.7 Quick Start Guide 33
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