MacroModel Reference Manual - ISP

Chapter 4: Operation CodesIf a SUBS command appears in the .com file with a zero-valued first argument, then Macro-Model looks for a file named filename.sbc, in which it expects to find SUBS, FXAT, ASL1,ASL2, and ASL3 commands. This file can be produced either manually or using Maestro.ASL1, ASL2 and ASL3 commands must be added manually. Additional SUBS commands withatom numbers can be used to direct additional atoms to be added to the set in the .sbc file.A typical use of both SUBS formats simultaneously might be simulating the binding of a largemolecule to a list of small molecules. The .sbc file would define the substructure and fixedatoms for the large molecule. The first SUBS command in the .com file would have a zerovaluedfirst argument and would set up the substructure for the large molecule. SubsequentSUBS commands would include the small molecules in the simulation. The input data files foreach job would contain the large molecule first, ensuring that its numbering scheme, like thatin the .sbc file, remains constant over the series of runs.If a negative number is given for any of arg1 through arg4, then the entire molecule containingthat atom number is defined as a part of the substructure. For MBAE calculations a .sbc fileshould be used to specify the substructure.SUBS commands with nonzero first arguments must come after READ commands. SUBScommands with zero first arguments must come before READ, because the .sbc file is readduring structure file reads.arg1Substructure atom number0 Obtain information from .sbc file; arg3 and arg4 are ignored.arg2File for substructure specification1 Use jobname.sbc.≠1Use current_rootname.sbc. For example, if a single rewind has beendone then current_rootname is jobname-out.>0 Atom number.arg2-4Substructure atom number>0 Atom number.arg5Add/Delete atoms0 Default, add the atoms listed to the substructure.−1Remove the atoms listed from the substructure.MacroModel 9.7 Reference Manual 65