MacroModel Reference Manual - ISP

Chapter 4: Operation CodesAUOP — AUto OPtionsWhen AUTO is used in conjunction with an MCMM, mixed MCMM/LMCS, mixed MCMM/LMC2, SPMC, or CGEN conformational search, AUOP may be used to modify the number ofsteps depending on some measure of the number of degrees of freedom present. AUOP shouldbe used immediately before the AUTO command.For CGEN by default the number of moves can also depend on ConfGen’s internal estimate forthe number of degrees of freedom. See CGO2 arg3 for more information.arg1Number of times global minimum is found>0 The search will terminate when the global minimum is found this many times. Notrecommended for ConfGen searches.arg3Exclude variable chirality atoms from chiral atom list0,1 Use full list of chiral atoms.2 Exclude atoms whose chirality can vary in solution. This currently only excludesnitrogen atoms bonded to 4 atoms one of which much be a hydrogen atom. Not recommendedfor ConfGen searches.arg5Number of steps 1 The search will use (number of degrees of freedom) * arg5 steps if this is less thanthe number of steps specified by the search command itself. For MCMM, mixedMCMM/LMCS, mixed MCMM/LMC2 and SPMC searches the number of degreesof freedom is given by the number of torsions (TORS) and molecules moved (MOLS)identified by AUTO. For CGEN jobs, the number of degrees of freedom can be estimatedthis way or from ConfGen’s internal estimate for the number of degrees offreedom, depending on the value of CGO2 arg3.LMCS — Low-Mode Conformational SearchThis method is described by Kolossváry and Guida [27, 28]. In tests so far, it has proved highlyefficient, and it has the advantage that ring structures and variable torsion angles do not have tobe specified. LMCS works by exploring the low-frequency eigenvectors of the system, which areexpected to follow “soft” degrees of freedom, such as torsions. It is, however, helpful tospecify independently movable molecules, by means of MOLS commands. Like the MCMMprocedure, LMCS may be seeded or restarted with multiple input structures, and LMCS may alsoMacroModel 9.7 Reference Manual 87