MacroModel Reference Manual - ISP

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Chapter 4: Operation Codesarg3Number of low-frequency modesLMC2 explores the first |arg3| modes. A maximum of 100 modes is allowed.0 Default: 30 (pure modes).0 Low-mode eigenvectors are recalculated every time the search finds a new globalminimum. The modes of the current global minimum are always used.
Chapter 4: Operation Codesarg6Allowable interatomic approach distanceFraction of sum of van der Waals radii used as a closest atomic approach limit. If avan der Waals pair comes closer together than this as the result of an LMCS move,the move is rejected before minimization.0 Default: 0.25>0 Other fraction.arg7Minimum distance (Å)Same as LMCS, except that the default values are different, depending on arg3.0 Default: 3 (Å) for single mode, arg3 >= 01 (Å) for mixed mode, arg3 < 0>0 Other value to be used.arg8Maximum distance (Å)Same as LMCS, except that the default values are different, depending on arg3.0 Default: 6 (Å) for single mode, arg3 >= 02 (Å) for mixed mode, arg3 < 0>0 Other value to be used.LOOP — protein LOOP conformation generationLOOP is a conformational search method for protein loops that works in conjunction with theMINI opcode in a manner similar to MCMM.Given a single protein structure LOOP attempts to generate candidate loop conformations usingeither the specified loop from the protein structure provided or an alternate user specifiedsequence for the loop. LOOP rapidly generates a candidate structure with the appropriate bondlengths and angles. In addition, heavy atoms in this structure (i.e., atoms heavier thanhydrogen) will not approach each other more closely than a specified distance. These candidatestructures are then energy minimized and can be checked for uniqueness in a manner analogousto that for MCMM. A more general discussion of the use of LOOP is available in Chapter 13of the MacroModel User Manual.MacroModel 9.7 Reference Manual 93
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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 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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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 Backgroundpath in
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Appendix G: MINTA BackgroundDirect
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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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