MacroModel Reference Manual - ISP

Chapter 4: Operation CodesAUTO — AUTOmatic setupPerform automatic setup for MCMM, MINI, SPMC, LMCS, LMC2, and combinations of MCMM withLMCS or LMC2, on the current structure. This procedure takes into account the current substructureinformation. The setup for MCMM is compatible with MCMM/LMCS and MCMM/LMC2. In addition,it can be applied in a serial manner (across different molecules in the input structure file)in MCMM, MCMM/LMCS, and MCMM/LMC2 serial searches, but not in pure LMC2 serial searches.AUTO is currently incompatible with LOOP and must be used carefully with MBAE. In addition,AUTO is incompatible with frozen atoms unless a substructure is being used.Note:Serial searches can generate large numbers of output structures, and the resultingoutput structure file can be large enough to exceed file size limits.AUTO should be preceded by the MSYM, MCMM, MCNV, MCOP, LMCS, LMC2, SPMC, SUBS, andREAD opcodes, if present, and is best placed just before the MINI line in the .com file.The type of calculation in use is detected automatically. For MINI calculations AUTO sets upcomparison atoms, chiral atoms, and torsional constraints unless instructed not to. For MCMMcalculations AUTO sets up comparison atoms, chiral atoms, torsional constraints, moleculemoves, variable torsions, and ring closures. For LMCS and LMC2 calculations, molecule moves,variable torsions, and ring closures are set up but not used, unless the setup is turned off. Seriesof bonded atoms that connect fixed or frozen atoms in substructures have ring closure bondscreated within them to prevent rotation of fixed or frozen regions. Failure to find such a ringclosure turns off all variable torsions in the SUBS atoms connecting such regions.AUTO arg8 controls the extent to which variable torsions are applied to the input structures.This option is relavent mostly to amide and ester linkages, and supplies a greater degree ofcontrol over sampling of standard and non-standard amides and esters. arg8=1 applies torsionmoves to the amide/ester linkage of non-standard groups like anhydrides, carbamates, hydrazones,and so on. Normal esters and amides are not sampled with this setting, but a torsionalconstraint is applied to them to ensure that the relative conformation of these groups is maintained.arg8=2 adds torsion moves to sample normal esters and amides in addition to amideand ester linkages of non-standard groups. arg8=3 adds torsion moves to C=N and N=N bonds,in addition to all amide and ester derivatives.In automatic setup, the maximum number of torsions varied at the same time is set to theminimum of arg2 of MCNV and the number of torsions present in the current system. If MCNVarg2 has not been set then the number of torsions present in the current system is used. In serialcalculations, the number of torsions varied at the same time is determined for each system.84MacroModel 9.7 Reference Manual