MacroModel Reference Manual - ISP

Appendix D: Force-Field File FormatFCH requires that ELE specify an equation (not none).For further explanation of how MacroModel handles charges, see Section 2.4 of the Macro-Model User Manual as well as the BDCO opcode in this manual.D.2.3ALT and SEL SpecificationThe lower parts (ALT, SEL) allow selection among various parameter types (O for original, M formodified, etc.) and among various alternative parameter sets (e.g., Allinger MM2 vs. OsawaMM2').The SEL (selection) descriptors above allow you to include (or exclude) the lines of the forcefields having certain labels. For example, associated with SEL 1 are three symbols O (for Original),M (for Modified), and A (for Added) which denote parameters which are original with thefield, modified from the original values or totally new entries. In the SEL lines above, all suchparameters are turned on, i.e., to be included into the force field which is read by the modelingprograms. If you wish to use only original parameters, delete the lines which select Modifiedor Added parameters (i.e., SEL 1 M and SEL 1 A). The O, M, and A symbols go with selectionswitch 1. SEL 2 has associated symbols 1, 2, and 3, signifying high-, medium-, and lowqualityparameters. If the SEL 2 2 and SEL 2 3 lines above are removed, the only high qualityparameters will be used in the calculation (however, there are no high quality parameters as yetfor many common substructures). You can add your own SEL switches starting with SEL 3 andchoose any symbols you wish for switching. The symbols you use are the same in the SEL linesabove and in the corresponding entries of the force field below. MacroModel allows a total of 5different SEL’s.The ALT (alternative) descriptors are similar to the SEL descriptors except that they selectsingle possibilities from among various options. We have defined ALT 1 to toggle between theoriginal MM2 parameters (signified by the symbol a) and the Osawa MM2' parameters (signifiedby the symbol b). By default, a is selected. You may notice that there are seemingly duplicateentries in the force field with slightly different parameters (MM2 and MM2'), these areswitched between by selecting the ALT symbol you want.Figure D.1 on page 196 shows how SEL and ALT options are encoded later, on an interactionby-interactionbasis, in the Main Parameter and Substructure sections of the force field. Eachinteraction may have values specified for the various SEL and ALT options. The SEL valuesshould be aligned below the columns labeled 1 2 3 4 5. The ALT number goes below Alt theparticular ALT symbol goes below the a. Comments should be used (30 characters maximum)since they are printed out along with the parameters in the output .mmo files containing detailedenergy listings. These comments are quite helpful in checking parameters.MacroModel 9.7 Reference Manual 195