MacroModel Reference Manual - ISP

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Chapter 3: Running MacroModel with the Simplified Input FileThe keywords for the simplified MacroModel input file are given in Table 3.2.Table 3.2. Keywords for the simplified MacroModel input fileKeyword SyntaxINPUT_STRUCTURE_FILE filenameFORCE_FIELD {MM2*|MM3*|AMBER*|AMBER94|OPLS|MMFF|MMFFs|OPLS_2001|OPLS_2005}SOLVENT {None|Water|Octanol|CHCL3}DIELECTRIC_CONSTANT constELECTROSTATIC_TREATMENT{Constant dielectric|Distance-dependent |Force-field defined }DescriptionName of the input structure file. NO DEFAULT.Force field. Default: OPLS_2005 . See the FFLD opcode.Solvent to use (continuum solvation model). Default:Water. See the SOLV opcode.Dielectric constant. Default: 1.0. See the FFLD opcode.Electrostatic treatment. Default: Constantdielectric. See the FFLD opcode.CHARGES_FROM {Force field|Structure file}CUTOFF {Normal|Extended|None}MINI_METHOD {PRCG|TNCG|OSVM|SD|FMNR|LBFGS}MAXIMUM_ITERATION nCONVERGE_ON {Gradient|Energy|Movement|Nothing}Source of partial charges to use for electrostatics.Default: Force field. See the CHGF opcode.Default: Normal. See the EXNB opcode.Minimization method. Default: PRCG. See the MINIopcode.Maximum number of iterations in a minimization.Default: 5000. See the MINI opcode.Quantity to use for testing the convergence of the minimization.Default: Gradient. See the CONV opcode.CONVERGENCE_THRESHOLD thresh Threshold for minimization convergence. Default: 0.05.See the CONV opcode.CONFSEARCH_METHOD {MCMM|Confgen|Lowmode|Mixed|mcmm|cgen|lmod|lmcs}MULTI_LIGAND {True|False}Conformational search method. Default: MCMM. See theMCMM, LMCS, LMC2, and CGEN opcodes.Specify whether the input contains multiple ligands(rather than a set of conformers). Used for serialsearches. Default: True.INCONFS_PER_SEARCH nconf Number of input conformations per search. Default: 0.See the MCOP opcode.28MacroModel 9.7 Reference Manual
Chapter 3: Running MacroModel with the Simplified Input FileTable 3.2. Keywords for the simplified MacroModel input fileKeyword SyntaxDescriptionOUTCONFS_PER_SEARCH mconfCONFSEARCH_STEPS nCONFSEARCH_STEPS_PER_ROTATABLEnBelow is an example simplified file for a conformational search:INPUT_STRUCTURE_FILE structure_path.maeCONFSEARCH_METHOD mcmmFORCE_FIELD OPLS_2001SOLVENT WaterDIELECTRIC_CONSTANT 1.0CHARGES_FROM Force fieldCUTOFF NoneMINI_METHOD PRCGOUTCONFS_PER_SEARCH 1CONFSEARCH_STEPS 200MAXIMUM_ITERATION 500CONVERGE_ON GradientCONVERGENCE_THRESHOLD 0.05ENERGY_WINDOW 5.0CONFSEARCH_STEPS_PER_ROTATABLE 50ELECTROSTATIC_TREATMENT Constant dielectricNumber of output conformations per search. This valuemust be a positive integer. Default: 1. See the MCOPopcode.Number of steps to use in the conformational search.Default: 200. See Section 4.10 on page 83.Number of steps to use per rotatable bond in a conformationalsearch. Default: 50. See the AUOP opcode.ENERGY_WINDOW value Energy window for keeping conformers. Default: 5.0.See the DEMX opcode.MacroModel 9.7 Reference Manual 29
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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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