MacroModel Reference Manual - ISP

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Contents2.2.1.2 Putting MacroModel to Sleep.................................................................. 182.2.1.3 Triggering an Interim Job Summary ........................................................ 192.3 Network-Distributed Processing .......................................................................... 192.3.1 Load Balancing ................................................................................................. 202.3.2 Types of Distributed Processing........................................................................ 202.3.3 MacroModel-Based Distributed Processing...................................................... 202.3.3.1 Internal Distribution................................................................................ 212.3.3.2 External Distribution............................................................................... 23Chapter 3: Running MacroModel with the Simplified Input File ........... 27Chapter 4: Operation Codes......................................................................................... 314.1 File Reading and Writing........................................................................................ 314.2 Selection of Force Field, Nonbonded Cutoffs, and Solvation Treatment ..... 334.3 Program Flow Control ............................................................................................ 444.4 Hydrogen Addition and Deletion .......................................................................... 454.5 Energy Calculation.................................................................................................. 454.6 Energy Minimization ............................................................................................... 524.7 Constrained Energy Minimization........................................................................ 634.8 Conformational Comparison................................................................................. 744.9 Coordinate Manipulation........................................................................................ 814.10 Conformational Searching................................................................................... 834.11 Molecular Dynamics and Monte Carlo Simulations...................................... 1174.12 Free-Energy Perturbation .................................................................................. 1354.13 Monte Carlo Simulation...................................................................................... 1374.14 Docking ................................................................................................................. 1384.15 Miscellaneous Commands and Debugging.................................................... 1414.16 ConfGen ................................................................................................................ 155ivMacroModel 9.7 Reference Manual
ContentsChapter 5: MINTA............................................................................................................... 1655.1 Overview ................................................................................................................. 1655.2 Introduction to MINTA........................................................................................... 1665.3 MINTA Methodology.............................................................................................. 1685.4 MINTA Commands................................................................................................. 1695.5 Notes........................................................................................................................ 1725.6 Working Examples ................................................................................................ 1735.6.1 Cyclononane ................................................................................................... 1735.6.2 Glucose........................................................................................................... 1755.6.3 Vancomycin..................................................................................................... 176Appendix A: MacroModel Test Suites .................................................................. 177Appendix B: MacroModel Benchmark Suites ................................................. 179Appendix C: Atom and Bond Types....................................................................... 181C.1 The atom.typ File ................................................................................................. 181C.2 MacroModel Bond Types .................................................................................... 181C.3 MacroModel Atom Types .................................................................................... 182Appendix D: Force-Field File Format.................................................................... 189D.1 Organization of the Force-Field File ................................................................. 189D.2 Introductory Section ........................................................................................... 190D.2.1 Equation Specification .................................................................................... 191D.2.2 Charge Processing ......................................................................................... 194D.2.3 ALT and SEL Specification ............................................................................. 195D.2.4 Atom Type Equivalencies................................................................................ 197D.3 Main Parameter Section ...................................................................................... 197D.3.1 Interactions ..................................................................................................... 197D.3.2 Adding New Parameters................................................................................. 206MacroModel 9.7 Reference Manualv
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Chapter 4: Operation Codes4.15 Misc
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Chapter 4: Operation Codes4.16 Conf
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Chapter 4: Operation Codesarg7Minim
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Chapter 4: Operation CodesConfGen i
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Chapter 4: Operation Codesarg6Maxim
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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: MINTAconformational sear
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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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