MacroModel Reference Manual - ISP

Chapter 4: Operation CodesFor example, if a molecule has four carboxylates and a trimethyl ammonium, then one wouldinclude five ATEQ commands, 4 for the carboxylates (2 equivalent atoms) and 1 for the trimethylammonium (3 equivalent atoms) if all atoms were included in COMP commands. Alternatively,such symmetrical atoms may be left out of the comparison lists. For high symmetrycases, it is better to replace ATEQ with NSEQ, NSRO, and NSRF commands. In such cases abetter alternative would be to use MSYM.In applying the ATEQ commands, the program will generate all permutations of equivalencedatoms to try for a near perfect geometrical match (i.e., find a duplicate conformer). Such anapproach will generate, inter alia, some nonsense permutations with clustered equivalent atoms(e.g., phenyl rings) but such permutations will never match and do not cause problems.Turning on DEBG 81 causes full information to be printed.arg1arg2-4Atom number of atom having other equivalent atomsAtom numbers of atoms equivalent to arg1NSEQ — Numbering System EQuivalenciesWe suggest using MSYM rather than specifying atom equivalences using NSEQ.This command allows the user to list alternative numbering systems for the molecule. For eachalternative numbering system, you will need as many NSEQ commands as you have COMPcommands. The COMP command can be considered as the original numbering system of thecomparison atoms. Each block of NSEQ commands corresponds an alternative numberingsystem for the comparison atoms listed in the COMP command. For united atom butane forexample, the COMP command might contain arg1-4 as 1 2 3 4, then the NSEQ command wouldcontain as the only possible alternative numbering system 4 3 2 1. An alternative to this simplecase would be to use NSRF. See the MacroModel User Manual for more complex examples.arg1-4Equivalent atom numbersNSRO — Numbering System ROtationWe suggest using MSYM rather than specifying atom equivalences using NSRO.This is intended primarily for use on symmetrical cyclics. This feature will cause the programto compare not only corresponding atoms, but also all possible rotations of the numberingsystem. Used with completely symmetrical systems such as cycloalkanes with the comparisoncommand, arg1 should be 1. Used with systems like 18-crown-6, arg1 should be 3 (note thatthis will not eliminate all duplicates with 18-crown-6—to do this, use the NSEQ commands).NSRO automatically turns on the NSRF option so that enantiomeric conformations are eliminated(this feature can be disabled with the NANT command). All atoms in the ring beingMacroModel 9.7 Reference Manual 79