MacroModel Reference Manual - ISP

Chapter 4: Operation CodesTOPN — Temporary file OPeNOpens the temporary coordinate file filename.tmp, where filename is the stem of the input filename. This command is typically used to recover the structures saved during a failed MULT orMCMM run by combining the atom connection table from the input file and atomic coordinatesfrom the .tmp file. A typical recovery command file is:filename.maefilename-out.maeDEBG 1READTOPN 100BGINTREDWRITENDThis command file opens the filename.mae structure file and the filename.tmp temporary file,reads in the first 100 coordinate sets from the temporary file, and writes the correspondingstructures to the output structure file, filename-out.mae.Arg1ofTOPN is the number of structuresto be read from the temporary file. See the end of the failed job log file to find thisnumber; however, be aware that the last structure in the .tmp file may be corrupted, dependingon the nature of the failure of the previous job.If this operation is to be used to recover structures from a run which used the SUBS command,then the SUBS commands in the original run must be included immediately after the READcommand in the command list above.arg1Number of atomic coordinate sets to be read from the .tmp fileMMOD — Maestro-macroMODel interactionDirects MacroModel to write a filename-mon.mae file, where filename is the stem of the .comfile name, for interaction with the Maestro GUI.Note:Note:This file conveys the structural information to Maestro so that the molecular structuredisplayed can updated while the job is running. Note that Maestro uses the .log filefor the textual information displayed in the Monitor panel.The writing of structural files can slow MacroModel down tremendously, especially onNFS-mounted filesystems. Thus, lowering the frequency of writing, or eliminating itentirely by removing the MMOD command, is worth considering for long jobs.32MacroModel 9.7 Reference Manual