MacroModel Reference Manual - ISP

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Chapter 1: Capabilities and New Features• Torsional potentials for highly strained conformations in which three of the atoms at oneend of the torsion become collinear can cause problems during minimizations. The torsionalpotential is damped as either triplet of atoms at the end of the torsion becomes linear.The strength of the damping can be controlled via arg8 of FFLD.1.2.2 Energy Minimization Methods• Large and small molecules.• Single or multiple structures.• Full structure or substructure.• Substructures can be specified using ASL expressions.• Positional, distance, and angular constraints.• Choice of steepest descent (SD), Powell-Reeves conjugate gradient (PRCG), truncated-Newton conjugate-gradient (TNCG), Oren-Spedicato variable metric (OSVM), fullmatrixNewton-Raphson (FMNR), and Limited Broyden-Fletcher-Goldfarb-Shanno(LBFGS) minimization methods.• Enhanced saddle-point searching (see the MINI command on page 52).• Eigenvalue minimum testing and vibrational frequencies.• Visualization of normal modes (VIBR and VBR2 ).• Harmonic-entropy free-energy calculations.• Greater control over intermediate output during minimization: see MINI command.• Explicit saddle-point search method (see the SDLP command on page 61).• The FXAT command has facilities which allow constraints to be relaxed in a stepwisemanner. Minimization may be performed at each stage. This is useful in refining poorlyinitialized structures which may have been derived from NMR or low-resolution crystallography,or from homology modelling.• The LCPO method, our accurate analytical surface-area computation method, is parameterizedfor metal atoms. DEBG 91 uses the old surface area method.• Additional LCPO parameters allow use of LCPO surface-area calculation with a broadervariety of atom types.• Automatic sequential minimization using multiple minimizer methods (MWRT).4MacroModel 9.7 Reference Manual
Chapter 1: Capabilities and New Features1.2.3 Conformational Searching and Comparison• Monte Carlo (MCMM) or systematic methods (SPMC).• Low-mode search method (LMCS).• Large-scale low-mode search method (LMC2). This facility extends the LMCS methodologyto systems large enough to encompass entire proteins.• ConfGen (CGEN). This is a separately-licensed module for rapidly and systematically generatingconformations of ligand-like molecules.• Acyclic, multicyclic, macrocyclic structures.• Internal coordinate searching.• Molecular docking (translation/rotation) searches.• Local or global conformational searches.• Duplicate conformer elimination.• The MSYM opcode uses the numbering symmetry library mmsym which automatically andmore generally identifies a suitable numbering order for use in comparing molecular conformations.• Elimination of redundant conformers using positional and energetic comparisons (ADDC)without changing internal geometry. Jaguar energies may be used in this process.• Automatic setup using the AUTO opcode is supported for Monte Carlo searches (MCMM),systematic searches (SPMC), low-mode searches (LMCS), large-scale low-mode searches(LMC2), and combinations of MCMM with LMCS or LMC2. Automatic setup may also be usedto conduct separate searches on each structure in the input structure file (serial searches)for all of these methods except those involving LMC2. Serial searches employing LMC2 arenot supported. The use of AUTO with LOOP is not supported, and if it is used with MBAE, itshould be used with caution.• Constrained searches.• Ability to initialize a new search from the output of a previous, partial search.• Ability to trigger a summary of search results so far while the program is running.• LIGB command allows configurational search about a metal coordination center.• LOOP. A fast method for generating candidate protein loop conformations based on thetweak method, using the sequence from the protein structure provided or an alternatesequence.MacroModel 9.7 Reference Manual 5
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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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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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