MacroModel Reference Manual - ISP

Chapter 4: Operation Codesarg7Comparison list inclusion0 Include heavy atoms.1 Include heavy atoms and hydrogens bonded to oxygen atoms.2 Include all atoms.3 Include only ring atoms. If no ring atoms are found, include heavy atoms and hydrogensbonded to oxygen atoms.arg8Comparison atom reporting1 Report comparison atom identification.CRMS — Convergence RMSSets the geometric criterion which defines two structures to be identical within a conformationalsearch or a multiple minimization. Despite the command name, the program uses as itscriterion not the root-mean-square interatomic distance after optimal rigid-body superpositionof a pair of structures, but rather the maximum distance between corresponding atoms aftersuperposition.arg1Maximum atomic separation (Å)If very small deviations are used (e.g., arg1 = 0 or 1), then some duplicate structuresmay be retained due to incomplete convergence in energy minimization.0 .25 (default value)1 .102 .20n 0.1narg5Maximum energy difference for geometric comparisonIf two structures differ by an energy greater than this value, geometric comparison isnot attempted; the structures are considered different based on the fact that the energiesdiffer.0 4.184 kJ/mol.