MacroModel Reference Manual - ISP

Chapter 2: Running MacroModel2.1.4 The .com FileTo run a MacroModel job, a command file (.com file) and a molecular structure file arerequired. The .com file generally has the name filename.com, where filename is a valid filenameprefix. The .com file contains the name of the input structure file, the intended name ofthe output structure file, and a list of operation codes (“opcodes”) telling MacroModel whichoperations are to be performed and in which order they are to be performed.The general format of a command file for MacroModel is:filename.maefilename-out.maeOPCD IIIIII IIIIII IIIIII IIIIII FFFFF.FFFF FFFFF.FFFF FFFFF.FFFF FFFFF.FFFFOPCD IIIIII IIIIII IIIIII IIIIII FFFFF.FFFF FFFFF.FFFF FFFFF.FFFF FFFFF.FFFFOPCD IIIIII IIIIII IIIIII IIIIII FFFFF.FFFF FFFFF.FFFF FFFFF.FFFF FFFFF.FFFFThe example above has been modified below to show the column numbers:filename.maefilename-out.mae12345678 13 20 27 34 41 47 52 58 63 69 74|||||||| | | | | | | | | | | |VVVVVVVV V V V V V V V V V V VOPCD IIIIII IIIIII IIIIII IIIIII FFFFF.FFFF FFFFF.FFFF FFFFF.FFFF FFFFF.FFFFOPCD IIIIII IIIIII IIIIII IIIIII FFFFF.FFFF FFFFF.FFFF FFFFF.FFFF FFFFF.FFFFOPCD IIIIII IIIIII IIIIII IIIIII FFFFF.FFFF FFFFF.FFFF FFFFF.FFFF FFFFF.FFFFFor comparison, column numbers have also been added to the example below, which is takenfrom an actual .com file:filename.maefilename-out.mae12345678 13 20 27 34 41 47 52 58 63 69 74|||||||| | | | | | | | | | | |VVVVVVVV V V V V V V V V V V VMMOD 0 1 0 0 0.0000 0.0000 0.0000 0.0000FFLD 10 1 0 1 1.0000 0.0000 0.0000 0.0000BDCO 0 0 0 0 20.0000 99999.0000 0.0000 0.0000READ 0 0 0 0 0.0000 0.0000 0.0000 0.0000CONV 2 0 0 0 0.0500 0.0000 0.0000 0.0000MINI 1 0 500 0 0.0000 0.0000 0.0000 0.0000This file would have a name such as jobname.com and, if so, would be submitted from thecommand prompt with a command such as$SCHRODINGER/bmin job_nameMaestro uses a similar command for computations prepared with the interface.2.1.4.1 File SpecificationsThe first line of the instruction file above is the name of the input structure file. The resultingoutput structure file is given the name listed on the second line of the instruction file. The input14MacroModel 9.7 Reference Manual