MacroModel Reference Manual - ISP

MacroModel Reference ManualChapter 1Chapter 1:Capabilities and New Features1.1 General DescriptionThe original MacroModel graphical user interface (GUI) is no longer supported as of Macro-Model 7.2. It was replaced by Maestro, the GUI for all Schrödinger’s products. Therefore, theMacroModel name now refers both to what was formerly called the BatchMin executable, andto the software package containing that executable and the XCluster program.MacroModel is the batch-mode molecular modeling computational facility for use withMaestro. It is designed to minimize the energy of one structure or a series of structures, toeliminate duplicate conformations, to do conformational searches, and to conduct moleculardynamics simulations, including free-energy perturbation methods and mixed-mode MonteCarlo/stochastic dynamics procedures. MacroModel jobs may be started from the MaestroGUI, or may be run from the command-line. Some MacroModel features are not availablefrom the Maestro interface. This manual attempts a complete description of MacroModel’sfacilities.1.2 Energetic Calculations1.2.1 Force Fields and Energy Equations• MM2*, MM3*, AMBER*, and OPLS* force fields (enhanced and/or modified versionsof the corresponding native force-fields; see Appendix D for implementation differences).• Native OPLS_2001 1 (formerly named OPLS-AA).• Native OPLS_2005 1 .• Native MMFF94 and MMFF94s.• Native Amber 4.1 (AMBER94).• Automatic checking and adjustment of formal charges and bond orders in calculationsinvolving MMFF, MMFFs, and OPLS-AA force fields. This feature is disabled by DEBG191.1. In some places in this manual, the OPLS_2001 and OPLS_2005 force fields will be referred to collectively asOPLS-AA.MacroModel 9.7 Reference Manual 1