MacroModel Quick Start Guide - ISP

MacroModel Quick Start GuideChapter 1Chapter 1:Getting Started1.1 About MacroModelMacroModel 9.7 is a general purpose, force-field-based molecular modeling program withapplicability to a wide range of chemical systems. MacroModel provides multiple advancedmethods to aid in the understanding of chemical structure, energetics, and dynamics. A largeselection of force fields is included, along with the latest technical advances introduced into theOPLS force fields. Numerous minimization methods are available, enabling geometry optimizationsfor a broad selection of structural classes. A wide range of methods is available forconformational searching, which allows efficient sampling of the potential energy surface forlow-energy structures, including entire proteins. Solvation effects can be accounted for usingthe efficient continuum solvation model in MacroModel. Additional advanced features includemolecular dynamics simulations, free-energy perturbation simulations, and pure- and mixedensemblesampling methods.1.2 About this ManualThis manual contains exercises designed to help you learn the basic tasks for preparing andinitiating MacroModel calculations from Maestro. Once you have worked through these exercises,you will have an understanding of the basic MacroModel features. The exercises aredivided into groups:• Chapter 2 contains exercises on a number of basic operations in Maestro.• Chapter 3 contains exercises on the calculation and minimization of the energy.• Chapter 4 contains exercises on conformational searching.• Chapter 5 contains exercises on various other MacroModel capabilities.The exercises contain only the information required for basic understanding and to completethe task at hand. For more information about a particular MacroModel feature, see the Macro-Model User Manual. To learn more about the command line MacroModel and MacroModeloperation codes, see the MacroModel Reference Manual.Maestro comes with automatic context-sensitive help (Auto-Help), Balloon Help (tooltips), anonline help facility, and a set of manuals. For a tutorial introduction to the basic features ofMaestro, see the Maestro Tutorial. For information on using Maestro, see the Maestro onlinehelp, the Maestro Overview, or the Maestro User Manual.MacroModel 9.7 Quick Start Guide 1