MacroModel Reference Manual - ISP

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References39. Ryckaert. J.-P. Special geometrical constraints in the molecular dynamics of chainmolecules. Mol. Phys. 1985, 55, 549.40. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R.Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984, 81, 3684.41. van Gunsteren, W. F.; Berendsen H. J. C. A leap-frog algorithm for stochastic dynamics.Mol. Simul. 1988, 1, 173.42. Kolossváry, I. Evaluation of the Molecular Configuration Integral in All Degrees ofFreedom for the Direct Calculation of Conformational Free Energies: Prediction of theAnomeric Free Energy of Monosaccharides. J. Phys. Chem. A 1997, 101, No. 51, 9900-9905.43. Kolossváry, I. Evaluation of the Molecular Configuration Integral in All Degrees ofFreedom for the Direct calculation of Binding Free Energies: Application to the EnantioselectiveBinding of Amino Acid Derivatives to Synthetic Host Molecules. J. Am.Chem. Soc. 1997, 119, 10233-10234.44. Kolossváry, I. Mode Integration (MINTA): A Method for Selecting a Molecule Basedon Conformational Free Energy of One Molecule for Another Molecule. U.S. Patent 08/940, 145, September 29, 1997.45. Keseru, Gy.; Kolossváry, I. Molecular Mechanics and Conformational Analysis in DrugDesign; Blackwell Science: Oxford, 1999; Chapter 7.46. Williams, D. H. Structural studies on some antibiotics of the vancomycin group, and onthe antibiotic-receptor complexes, by proton NMR. Acc. Chem. Res. 1984, 17, 364.47. Cohen, M. L. Epidemiology of drug resistance: Implications for a post- antimicrobialera. Science (Washington, D.C.) 1992, 257, 1050.48. Mackay, J. P.; Gerhard, U.; Beauregard, D. A.; Westwell, M. S.; Searle, M. S.; Williams,D. H. Glycopeptide Antibiotic Activity and the Possible Role of Dimerization: A Modelfor Biological Signaling. J. Am. Chem. Soc. 1994, 116, 4581.49. Dunayevskiy, Y. M.; Lyubarskaya, Y. V.; Chou, Y.-H.; Vouros, P.; Karger, B. L. SimultaneousMeasurement of Nineteen Binding Constants of Peptides to Vancomycin UsingAffinity Capillary Electrophoresis-Mass Spectrometry. J. Med. Chem. 1998, 41, 1201.50. Slater,J.C.; Kirkwood, J.G. The van der Waals forces in gases. Phys. Rev. 1931, 37, 682.51. Weiner, P. K.; Kollman, P. A. AMBER: Assisted Model Building with Energy Refinement.A General Program for Modeling Molecules and Their Interactions. J. Comput.Chem. 1981, 2, 287.240MacroModel 9.7 Reference Manual
References52. Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. J. J. Phys. Chem. B2001, 105, 6474.53. Weiser, J.; Holthausen, M. C.; Fitjer, L. J. Comp. Chem. 1997, 18, 1264.MacroModel 9.7 Reference Manual 241
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MacroModel Reference ManualMacroMod
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ContentsDocument Conventions ......
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ContentsChapter 5: MINTA...........
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Document ConventionsIn addition to
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MacroModel Reference ManualChapter
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Chapter 1: Capabilities and New Fea
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Chapter 2: Running MacroModelTable
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Chapter 2: Running MacroModelstruct
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Chapter 2: Running MacroModel2.2 Jo
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Chapter 2: Running MacroModelfile
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Chapter 2: Running MacroModelusing
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Chapter 2: Running MacroModel2.3.3.
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Chapter 2: Running MacroModelalso s
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Chapter 3: Running MacroModel with
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Chapter 4: Operation Codesarg1Frequ
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Chapter 4: Operation Codesarg3Hydro
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Chapter 4: Operation CodesTable 4.1
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Chapter 4: Operation CodesLimitatio
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Chapter 4: Operation Codesarg3Note:
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Chapter 4: Operation Codes2 Use for
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Chapter 4: Operation Codes1 The cur
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Chapter 4: Operation Codes1 Use fas
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Chapter 4: Operation Codesway on th
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Chapter 4: Operation Codes
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Chapter 4: Operation CodesIf solvat
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Chapter 4: Operation CodesFMNR has
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Chapter 4: Operation Codesarg1Listi
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Chapter 4: Operation Codesnarg3For
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Chapter 4: Operation Codesarg3 Symm
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Chapter 4: Operation Codes4.7 Const
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Chapter 4: Operation CodesIf a SUBS
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Chapter 4: Operation CodesASL3 —
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Chapter 4: Operation Codes>0 Specif
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Chapter 4: Operation CodesThe const
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Chapter 4: Operation Codesarg2Clear
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Chapter 4: Operation CodesADDC —
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Chapter 4: Operation Codesarg7Compa
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Chapter 4: Operation CodesFor examp
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Chapter 4: Operation Codesarg1arg2a
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Chapter 4: Operation Codes4 Rotate
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Chapter 4: Operation Codesarg1−1A
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Chapter 4: Operation CodesAUOP —
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Chapter 4: Operation CodesLMCS can
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Chapter 4: Operation CodesLMC2 is i
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Chapter 4: Operation Codesarg6Allow
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Chapter 4: Operation Codes• Rings
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Chapter 4: Operation Codesarg1Param
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Chapter 4: Operation Codes2 H×v is
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Chapter 4: Operation Codesarg8Spars
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Chapter 4: Operation CodesSPMC sear
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Chapter 4: Operation Codes0 Use set
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Chapter 4: Operation Codes−1arg5D
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Chapter 4: Operation Codesarg2 Line
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Chapter 4: Operation CodesSEED —
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Chapter 4: Operation Codesfrom with
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Chapter 4: Operation Codesarg1-4Ato
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Chapter 4: Operation CodesnWrite ev
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Chapter 4: Operation Codesarg3Molec
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Chapter 4: Operation Codes0 Time in
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Chapter 4: Operation CodesMDAP —
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Chapter 4: Operation CodesMHBD —
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Chapter 4: Operation CodesMDFT —
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Chapter 4: Operation Codesment. We
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Chapter 4: Operation Codesarg7Time_
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Chapter 4: Operation Codesarg6Inter
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Chapter 4: Operation Codes1 Do not
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Chapter 4: Operation Codesarg 8Maxi
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Chapter 4: Operation CodesThis comm
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Chapter 4: Operation Codes4.15 Misc
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Chapter 4: Operation Codes45 [NEW]
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Chapter 4: Operation Codes100 Set n
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Chapter 4: Operation Codes252 GV, c
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Chapter 4: Operation Codes931 Turns
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Chapter 4: Operation Codesarg2arg3a
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Chapter 4: Operation Codesarg1Numbe
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Chapter 4: Operation Codes4.16 Conf
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Chapter 4: Operation Codes−3do no
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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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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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Page 197 and 198: MacroModel Reference ManualAppendix
Page 199 and 200: Appendix D: Force-Field File Format
Page 231 and 232: Appendix E: The BMFF ProtocolBefore
Page 237 and 238: Appendix G: MINTA BackgroundL(s)
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Page 241 and 242: Appendix G: MINTA BackgroundDirect
Page 243 and 244: Appendix G: MINTA BackgroundPaulsen
Page 245 and 246: MacroModel Reference ManualReferenc
Page 247: References26. Sefler, A. M.; Lauri,
Page 251 and 252: Opcode IndexBold face page numbers
Page 253 and 254: Opcode IndexRRHO...................
Page 256: 120 West 45th Street, 29th FloorNew
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