MacroModel Reference Manual - ISP

MacroModel Reference ManualChapter 2Chapter 2:Running MacroModel2.1 Running MacroModel From the Command LineMacroModel jobs may be started from the Maestro GUI or from the command-line. The mechanismsfor running jobs from the command line are described in this chapter. You might wishto run MacroModel from the command line for any of the following reasons:• To exercise greater control over MacroModel behavior: not all of MacroModel’s functionalityis available from Maestro.• To perform a series of related MacroModel runs: it may be easier to edit an existing MacroModelcommand file than to set up each job separately from Maestro. Sometimes severaljobs are queued up and run from a shell script.• To debug an aberrant run: when a MacroModel run fails to do what is expected, a simplecommand can sometimes be added to the MacroModel command file to instruct the programto give more detailed output.MacroModel jobs run under Schrödinger’s Job Control facility. This facility manages theexecution and monitoring of jobs, and handles the input and output files and the incorporationof results into a Maestro project. The Job Control Guide describes how to set up the informationneeded for Job Control to run on the computers to which you have access. It includesinformation on remote hosts, clusters, and batch queues.2.1.1 Environment VariablesWhenever MacroModel is run, the UNIX environment variable SCHRODINGER must be set tothe directory where MacroModel was installed. In addition, there are other environment variablesthat can be set to override default resource values. See Appendix B of the Job ControlGuide for more information.By default, the Schrödinger job control facility uses ssh to communicate between remotenodes. A mechanism exists to specify alternative commands for remote command execution.The environment variable SCHRODINGER_RSH should be set to the alternate application, whichneed to support the same basic command-line syntax as ssh. Commands need to be passedwithout asking for a password or requiring any other user interaction. For more information,see Section 6.2 of the Installation Guide.MacroModel 9.7 Reference Manual 11