MacroModel Reference Manual - ISP

Chapter 2: Running MacroModel2.1.2 Command-line SyntaxMacroModel is run from the command-line by executing the shell script bmin, which islocated in the $SCHRODINGER directory, or the macromodel script, also located in this directory.The macromodel script and its input file are described in Chapter 3; this section focuseson the bmin script. The bmin script determines the proper executables to run for the host beingused. Additional utility programs are provided in the $SCHRODINGER/utilities directory.The $SCHRODINGER/macromodel-vversion/data directory also contains a number of files(such as force field files) that MacroModel needs in order to run.Whether MacroModel is started from the shell or from Maestro, if copies of the force field,solvent or atom type files exist in the $HOME/.schrodinger directory, they override theversions of these files in the $SCHRODINGER/macromodel-vversion/data directory. If copiesof the force-field, solvent and/or atom-type files exist in the local directory, they override anyversions of these files in both the $HOME/.schrodinger and $SCHRODINGER/macromodelvversion/datadirectories.The syntax for the bmin command is as follows:$SCHRODINGER/bmin [options] jobnameThe options for the bmin command are listed in Table 2.1. The standard Job Control optionsare also supported—see Section 2.3 of the Job Control Guide. Additional diagnostic options,which do not run the job but provide information, are also given in the section mentioned. Inparticular, you should note the syntax of the -HOST option, which is used to specify the list ofhosts used for the job.Table 2.1. Options for the bmin command.Option-DEBUGGER debugger_name-DEBUG2-h[elp],-HELP-HOSTFILE hostfilename-INTERVAL value-LOCAL-NO_REDIRECTDescriptionRun bmin in the foreground with a debugger calleddebugger_name.Print out debugging information from the scripts used to start bmin.Show usage message.The name of the hosts file to use for this run. Default isschrodinger.hosts.The maximum time in seconds for updating the monitoring files.Do not use a temporary directory keep the files. Keep files in thelocal directory.Run in the foreground and send output to standard output.12MacroModel 9.7 Reference Manual