MacroModel Reference Manual - ISP

Chapter 4: Operation Codesrotated must be listed in the COMP commands. Furthermore the atoms listed in COMPcommands must be in the order in which they occur in the ring. Atoms not in the ring (hydrogensor other substituents) should not be listed.NSRO must come before READ or TRED commands and after COMP commands.arg1Rotation incrementThe number of atoms by which a ring must be rotated to bring equivalent atoms intosuperimposition. (Default: 1).NSRF — Numbering System ReFlectionWe suggest using MSYM rather than specifying atom equivalences using NSRF.If invoked, this feature will cause the program to compare not only corresponding atoms butalso numbering system reflections. Used with symmetrical structures such as normal acyclicalkanes with the comparison command. This command reverses the ordering of the atoms inthe COMP commands for comparison purposes, thus atoms in the COMP commands must begiven in the order of the atoms in the chain.NSRF must come before READ or TRED commands.NANT — do not consider eNANTiomers to be duplicatesOrdinarily, enantiomers are considered identical for the purpose of conformational comparisons.This command, which alters this behavior, takes no arguments.DEMX — Delta-E MaX energy windowingDEMX sets a window for permissible energy above the lowest-energy conformation. Thiscommand discards any structure that is more than arg5 kJ/mol above the minimum energyconformation. Since more than one force field may be used in a command procedure, arg1 is acode that is matched to a corresponding “energy code” in a MINI command. DEMX is used withMULT and MCMM commands. If no DEMX is used, then all energy minima will be kept regardlessof their relative energies. We use this command to limit the energy range of the conformersprinted out at the end of the procedure. We suggest a value of 25.0 kJ/mol (ca. 6 kcal/mol) forarg5 to prevent output of high-energy structures. If you plan to do a subsequent solvation treatment,a 50.0 kJ/mol window may be more appropriate to allow for major reordering of structureson inclusion of solvation. However, it is better to include solvation (SOLV command)directly in the minimization.A second energy window may be set in arg6 (suggested value 1.5-2 times that in arg5), whichis used to reject structures before complete minimization by a check of the relative energy atiteration number arg2. Aborting the minimization of structures whose energies appear too largepart way through the minimization makes the overall procedure faster.80MacroModel 9.7 Reference Manual