MacroModel Reference Manual - ISP

Appendix D: Force-Field File FormatNote the use of parentheses to identify atoms off the linear backbone as represented. Quinolinecould be:N=C-C=C-C=C(-1)-C=C-C=C-5For the quinoline above to match, it would have to have the connectivity and bonding exactlyas drawn above. Thus the user would always have to draw the correct resonance structure forthe parameters to be found. As an alternative, we generally specify the atom type more exactlyto designate the atomic hybridization and use wild card bonds for all the connectivity. Thus anyresonance form of quinoline would match the following:N2*C2*C2*C2*C2*C2(*1)*C2*C2*C2*C2*5D.4.2.2Chain BranchingAs a further example of the use of parentheses, methylcyclobutane could have any of thefollowing linear notations:C(-C)-C-C-C-1C-C-C-C(-C)-1C-C-C-C(-1)-CC-C(-C)-C-C-1Parentheses may be nested. Isopropylbenzene could be:C=C(-C(-C)-C)-C=C-C=C-1Threonine could be:N-C(-C(-C)-O-H)-C=OD.4.2.3Optional AtomsOptional atoms may also be specified within the linear notation so that the substructure willmatch whether or not the optional atom is found. Optional atoms with associated bonds are putin square brackets ([ ]). In the substructure below, serine would be identified whether or not theoptional hydrogens were present in the structure:N[(-H)]-C(-C-O[-H])-C=OParameters are assigned for optional atoms if the atoms are explicitly present in the molecule.If the optional atoms are absent, the constants involving those atoms will not be used in reassigningthe interaction constants previously assigned by the first part of the force field (1-4atom interactions). Another way to accomplish the same end is to omit the optional atoms butto include the parameters involving the hydrogens as off-substructure interactions (see below).MacroModel 9.7 Reference Manual 213