MacroModel Reference Manual - ISP

Appendix D: Force-Field File Formattypes for that substructure, if they exist, must precede the partial charge parameterline(s).D.4.2Substructure Linear NotationIn addition to the normal one- to four-atom descriptors of stretch, bend, and torsional substructuresused in molecular mechanics, MacroModel provides for description of more complexsubstructures. These are the “special substructures” given at the end of a MacroModel forcefield files. The description of the atomic connectivity is given by a simple linear notation whichresembles SMILES/SMARTS notation. Atoms and bonds are described as in normal interactionsbut up to 50 atoms (130 characters maximum) may comprise a substructure, and complicatedconnectivity, including wild-card and optional atoms, may be specified.Structures are described as a list of connected atoms and bonds; all atoms and bonds in thestructure must be explicitly included. Ethyl vinyl ether would be:C2=C2–O3–C3–C3The atom types are normal MacroModel atom types: C2 is sp 2 carbon, C3 is sp 3 carbon, and O3is non-carbonyl oxygen.Simple generalized atom descriptors may also be used; then the formula above would be:C=C–O–C–CYou may also use the equivalenced atom types to represent many different types of atoms.Generalized bond descriptors may also be used; for example, an asterisk (*) stands for a bondof any order:C*C-O-C-CThis could represent diethyl ether, ethyl vinyl ether or ethoxy acetylene.D.4.2.1Ring ClosureRing-forming bonds are added as a bond type followed by a number which specifies whichatoms are bound together. Cyclopentane is:C-C-C-C-C-1Thus the last (fifth) atom is bound to the first (-1); this signifies a single bond to the first atomin the substructure. Ring closure bonds can go only to atoms earlier in the substructure.Norbornane would be represented:C-C-C-C(-C-1)-C-C-1212MacroModel 9.7 Reference Manual