MacroModel Reference Manual - ISP

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ContentsD.3.3 Special Notes for AMBER............................................................................... 207D.3.4 Special Notes for MM2 and MM3 ................................................................... 210D.4 Substructure Section .......................................................................................... 211D.4.1 Use of Substructures ...................................................................................... 211D.4.2 Substructure Linear Notation.......................................................................... 212D.4.2.1 Ring Closure ....................................................................................... 212D.4.2.2 Chain Branching.................................................................................. 213D.4.2.3 Optional Atoms.................................................................................... 213D.4.3 Substructure Charge Processing.................................................................... 214D.4.4 Substructure Examples .................................................................................. 214D.4.5 Geometry-dependent Parameters .................................................................. 216Appendix E: The BMFF Protocol ............................................................................. 221E.1 Purpose ................................................................................................................. 221E.2 Overview ................................................................................................................ 221E.3 MMFF Considerations ......................................................................................... 223Appendix F: Format of .grd Files ............................................................................. 225Appendix G: MINTA Background............................................................................. 227G.1 Introduction .......................................................................................................... 227G.2 The Thermodynamic Cycle ................................................................................ 228G.3 Computational Methods ..................................................................................... 229G.4 References ............................................................................................................ 233References.............................................................................................................................. 237Opcode Index ........................................................................................................................ 243viMacroModel 9.7 Reference Manual
Document ConventionsIn addition to the use of italics for names of documents, the font conventions that are used inthis document are summarized in the table below.Font Example UseSans serif Project Table Names of GUI features, such as panels, menus,menu items, buttons, and labelsMonospace $SCHRODINGER/maestro File names, directory names, commands, environmentvariables, and screen outputItalic filename Text that the user must replace with a valueSans serifuppercaseCTRL+HKeyboard keysLinks to other locations in the current document or to other PDF documents are colored likethis: Document Conventions.In descriptions of command syntax, the following UNIX conventions are used: braces { }enclose a choice of required items, square brackets [ ] enclose optional items, and the barsymbol | separates items in a list from which one item must be chosen. Lines of commandsyntax that wrap should be interpreted as a single command.File name, path, and environment variable syntax is generally given with the UNIX conventions.To obtain the Windows conventions, replace the forward slash / with the backslash \ inpath or directory names, and replace the $ at the beginning of an environment variable with a% at each end. For example, $SCHRODINGER/maestro becomes %SCHRODINGER%\maestro.In this document, to type text means to type the required text in the specified location, and toenter text means to type the required text, then press the ENTER key.References to literature sources are given in square brackets, like this: [10].MacroModel 9.7 Reference Manualvii
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MacroModel Reference ManualChapter
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Chapter 5: MINTAthat energy well. N
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Chapter 5: MINTAature. Note that H
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Chapter 5: MINTA0 Numerical integra
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Chapter 5: MINTAtion (25,000 total
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MacroModel Reference ManualAppendix
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Appendix C: Atom and Bond TypesTabl
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Appendix D: Force-Field File Format
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Appendix E: The BMFF ProtocolBefore
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Appendix G: MINTA BackgroundL(s)
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Appendix G: MINTA BackgroundPaulsen
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MacroModel Reference ManualReferenc
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References26. Sefler, A. M.; Lauri,
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References52. Kaminski, G. A.; Frie
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Opcode IndexBold face page numbers
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Opcode IndexRRHO...................
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