MacroModel Reference Manual - ISP
MacroModel Reference Manual - ISP
MacroModel Reference Manual - ISP
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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: <strong>MacroModel</strong> Test Suites .................................................................. 177Appendix B: <strong>MacroModel</strong> Benchmark Suites ................................................. 179Appendix C: Atom and Bond Types....................................................................... 181C.1 The atom.typ File ................................................................................................. 181C.2 <strong>MacroModel</strong> Bond Types .................................................................................... 181C.3 <strong>MacroModel</strong> 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................................................................................. 206<strong>MacroModel</strong> 9.7 <strong>Reference</strong> <strong>Manual</strong>v