MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg1−1AUTO On/OffTurn off automatic setup.0 Turn on automatic setup and generate a new setup using the current system.1 Turn on automatic setup. If automatic setup is already on, use the existing setup.arg2−1Comparison atom setupUse existing list of comparison atoms.0 Use previous setting. If none exists, arg2 is set to 2.1 Create a new list of comparison atoms containing all non-hydrogen atoms.2 Create a new list of comparison atoms containing all non-hydrogen atoms andhydrogen atoms bound to oxygen atoms.3 Create a new list of comparison atoms containing all of the atoms.4 Create a new list of comparison atoms containing all non-hydrogen atoms. Also usedihedral angle differences involving polar H atoms (bonded to a O, S or N atom) inredundant conformer elimination. If the dihedral angles in two conformers differ bymore than a threshold (controlled by CRMS arg7) then the conformers are judged tobe distinct.5 Create a new list of comparison atoms containing all ring atoms. If no ring atomsare found, use heavy atoms and hydrogen atoms bonded to oxygen atoms.arg3−1Chiral atom setupUse existing list of chiral atoms.0 Use previous setting. If none exists, arg3 is set to 1.1 Create a new list of chiral atoms (overrides CHIG for the current structure).arg4−1Torsional constraintsUse existing list of torsional constraints.0 Use previous setting. If none exists, arg4 is set to 1.MacroModel 9.7 Reference Manual 85