MacroModel Reference Manual - ISP

Appendix D: Force-Field File Format...1 10 11 1.1683 4.6000v1 10 11 1.0740 4.6000...2 2 3 10 88.969 0.0600r2 2 3 10 88.969 0.00002 H1 3 10 88.563 0.0500r2 H1 3 10 88.563 0.0000The equilibrium bond length between substructure atom 4 and an off-substructure H1 is set to1.0712 Angstrom by default. If the optional C3 is present on atom 4, it is given the value1.0736 Angstrom, unless the 2-3-4-5 torsion falls between 120 and 240. In this situation, the4-H1 bond-length is set back to the default value. The two other torsional dependencies shownare straightforward.The lines beginning with r2 specify a test against the ring constraint. The 2-3-10 bendingforce-constant is set to 0.06 by default, but is set to zero instead if atoms 2 and 10 fall within aring of size 8 or less. This condition will be met in the internal Diels-Alder transition state. TheH1-3-10 bending force-constant (where H1 is an off-substructure hydrogen) is subject to asimilar test.The same mechanism can be used to specify the angular dependence of a parameter. The letterA in the second column of a force-field substructure line denotes such a dependence. The firstreal-number field specifies a central value, and the second specifies a range about it. Thismechanism can be used, for example, to set equilibrium bond angles in a trigonal bipyramidalcomplex to 90˚, 120˚ or 180˚, depending on whether each ligand pair is axial-equatorial, equatorial-equatorialor axial-axial. Usually, however, one uses the points-on-a-sphere approach(see VDWB) to model such systems.MacroModel 9.7 Reference Manual 219