MacroModel Reference Manual - ISP

Chapter 2: Running MacroModelThe facilities described in this section become inactive if DEBG 930 is specified, which is thedefault behavior. DEBG 931 may be specified to enable these facilities.You can interact with a running MacroModel job by creating a file in the directory from whichthe job was launched. One simple way to do this from the UNIX command line is to use theUNIX touch command:touch filename.sfxwhere filename is the filename prefix of the input file (usually the job name) and .sfx is a suffixthat depends on the action desired, as described in the following sections.2.2.1.1 Stopping MacroModelYou may wish to stop a MacroModel run before it has completed normally. For example, scrutinyof the log file generated so far may reveal that a conformational search is essentiallycomplete before the requested number of conformations have been generated. The job may ofcourse be killed from the UNIX shell by using the commandkill -9 pidwhere pid stands for the process identification number, which can be obtained through use ofthe UNIX ps command. If this is done, then MacroModel exits without doing its normalcleanup. This means, among other things, that output buffers will not be flushed, and thatscratch files, such as filename.tmp, will not be converted to final form, such as the ASCII filefilename-out.mae, and removed. This state of affairs also occurs when the system kills theMacroModel job or when the system crashes. Recovery from this state is possible by means ofthe TRED command, described in Chapter 4.There is, however, a gentler way to kill MacroModel—one which causes the process to carryout its normal clean-up operations. To do this, create a file called filename.stp in the directoryin which the MacroModel job was initiated. The .stp suffix is a mnemonic for “stop.” Macro-Model periodically checks for the existence of such as file, and, if it finds it, branches immediatelyto its normal cleanup and exit procedure. MacroModel removes the .stp file prior toexiting; thus the same job may be rerun if desired without first removing this file manually.2.2.1.2 Putting MacroModel to SleepOccasionally you might like to temporarily suspend the execution of a MacroModel job andrestart it later. One reason for doing this might be to obtain faster response time for an interactiveprogram, such as Maestro. This can be accomplished by creating a file in the directoryfrom which MacroModel was started called filename.slp; the .slp suffix is a mnemonic for“sleep,” and filename is the prefix of the input file. MacroModel periodically looks for the.slp file, and, if it finds it, suspends execution, except for periodically attempting to verify the18MacroModel 9.7 Reference Manual