MacroModel Reference Manual - ISP

Appendix D: Force-Field File Format-3C Pyranose sugar9 O3-C3-O3-C3-C3-C3-C3-C3-2-2aT 1 2 3 4 180.0000 60.00001 1 2 1.3000 5.0000 0.0000a1 1 2 1.4000 5.0000 0.0000This shows how parameters may be selected depending on the value of a torsion. Here, wewish to load one exocyclic O3-C3 bond length (1.3 Å) for an a-anomeric (axial) sugar, and adifferent bond length (1.4 Å) for a b-anomeric (equatorial) sugar. The entry beginning aTdefines a geometrical constraint which is to be tested just before the parameters are loaded. TheT defines the constraint as a torsion. The a could be any character (a-z, A-Z) and is used toassociate particular subsequent interaction lines with the constraint. The 1 2 3 4 torsionangle, because it is preceded with an a, will be subjected to the aT specification. The constrainttest will passed if the torsion angle of the equivalent atoms in the molecule is in the range 180˚60˚. For β-anomeric sugars, this torsion angle would be approximately 180˚ (anti). In theexample, the 1-2 bond (the first O3-C3 in the substructure) will be given a natural length of 1.3Å by default, but if the torsional constraint labeled “a” is met, it will be given the value 1.4Angstrom. This is specified by prefixing the interaction line containing this bond-stretchparameter value by the letter “a.” The the more specific (here a1') interaction line must comesecond in the list of substructure force field entries, since in these entries the last match foundoverrides the others. If the default value were given last, it would always be used.The following excerpt exhibits a more complex torsional dependence of several parameters,and also a dependence on whether several atoms are present in a ring. Here, parameters may bedependent upon three different torsions, given in the lines beginning with uT, vT, and wT, oronwhether the atoms in the molecule corresponding to substructure atoms 2 and 10 are in a ringof size eight or smaller, as specified in the line beginning with rR.-3C Diels-Alder TS (activ), Houk, JACS, 4796 (1992)9 O=C2-C2=C2[(-C3)].C2[(-H1)]=C2-C2=C2[(-H1)].3-2uT 2 3 4 5 180.0000 60.0000vT 8 9 10 11 180.0000 60.0000wT 9 8 6 7 180.0000 60.0000rR 2 10 8.0000...1 4 H1 1.0712 4.60001 4 H1 1.0736 4.6000 C300u1 4 H1 1.0712 4.6000 C300...1 6 7 1.1720 4.6000w1 6 7 1.0743 4.6000218MacroModel 9.7 Reference Manual