MacroModel Reference Manual - ISP

Chapter 2: Running MacroModelstructure file contains the molecular structure(s) of the molecules to be processed, and theoutput file will contain the structures after processing. The input and output structure files canbe named with any valid UNIX filename, as long as they differ.Note:The output structure file now uses the Maestro format regardless of the format used inthe input structure file. Specifying DEBG 6 forces MacroModel to use the Macro-Model format for the output structure file.In previous versions of MacroModel, the input and output structure file names were usuallynamed filename.dat and filename.out. Now that all Maestro formatted structure files are, bydefault, named with the .mae extension, Maestro now automatically names the input structurefile filename.mae and the output structure file filename-out.mae. We recommend using filename.maeand filename-out.mae for these files when Maestro-formatted files are used, so thatthe suffix reflects the format used in the file. The filename stem for the input file is often thesame as the filename prefix for the .com file. You can also use compressed Maestro files(.maegz or .mae.gz) for both input and output.In addition, any input substructure (.sbc) or velocity (.vel) files should contain the samestem as the input structure file. Similarly the output energy listing (.mmo), substructure, anddihedral drive (.grd) files should have the same stem as the output structure file. The output.log file contains the same stem as the .com file. Experienced users of MacroModel should beaware that this mechanism has not changed from previous versions of the program.The program allows full-path filenames up to 100 characters in length. The filename stemsneed not be identical for the input, output, and .com files, but they are the same in jobs set up inMaestro and it is usually most convenient to follow this convention. MacroModel may createvarious temporary files in the course of its work. The filename stem for these files is taken fromthe filename stem of the input file name.2.1.4.2 Operation Code SpecificationsThe remaining lines in the .com file provide the instructions to MacroModel about the type andorder of calculations to be performed. The opcode lines must be of the following fixed format:OPCD IIIII IIIII IIIII IIIII FFFFF.FFFF FFFFF.FFFF FFFFF.FFFF FFFFF.FFFFOPCD is a four-letter operation code (“opcode”) for a command; each line containing anopcode begins with a space. The eight fields after the OPCD are referred to as “arguments.”IIIIII represents an integer argument in Fortran I6 format (arg1-arg4), and FFFFF.FFFFrepresents a floating point argument in F10.4 format (arg5-arg8).Note:Arg5-arg8 require a decimal even when integer values are provided. Each opcodedefines a general command for MacroModel, and the integer and real-number argumentsspecify more specific operations or options. Any line containing an opcode canMacroModel 9.7 Reference Manual 15