The jaguar Command

You can use the jaguar command to perform the following tasks, among others:

Run a job on any machine at your site
Summarize results of a Jaguar job
Run special jobs such as Babel file conversion or NBO calculations

If Jaguar is installed on more than one machine at your site, you can use the jaguar command on one machine to run Jaguar jobs on another machine, even if you are not logged in to the second machine. This section describes in some detail how and when to use the jaguar command.

The syntax of the jaguar command is

jaguar [command] [options]

where command is any of the commands listed in Table 1. If the jaguar command is not in your path, you must precede it with $SCHRODINGER, i.e. $SCHRODINGER/jaguar. (This is not necessary on Windows.) The options may be given in any order, and may precede any options specific to the command. See Running Schrödinger Applications from the Command Line for general information on running from the command line.

Table 1. Commands for the `jaguar` command
Command	Description
`run [script.py] [options] input-files`	Start the Jaguar jobs whose input files are listed, using the specified script if given, and the specified run time options. The `run` command can be used to run any kind of Jaguar workflow or job.
`run jobname.recover`	Rerun a Jaguar job exactly as it was run the first time. If the job has subjobs, some of which failed, rerun only the failed subjobs.
`pka [options] input-file`	Start a Jaguar pK_a calculation. You can also run this with `run pka.py` instead of `pka`.
`babel [babel-options]`	Perform a file format conversion using Babel.
`nbo`	Run an NBO calculation [110, 111].
`results options`	Summarize results from the output file using the options specified. See Summarizing Jaguar Results for more information on this command.
`help`	Display a command syntax summary including a list of valid commands.

The input-files argument to the jaguar command is a list of names of Jaguar input files. The name must include the .in extension. Jaguar removes the .in extension to form the job name. For example, the command

jaguar run h2o.in

runs a Jaguar job with the job name h2o and the input file h2o.in.

In addition to running the commands listed in Table 1, you can use the jaguar command with the standard Job Control options listed in Running Jobs From the Command Line to obtain information about hosts available. For example, to determine which machines are available for running Jaguar jobs, enter the command

jaguar -HOSTS

The hosts listed are those in the schrodinger.hosts file that are being used by the jaguar command. If you find that the list of hosts is incomplete, you may need to edit the schrodinger.hosts file indicated on the first line of the command output. See The Hosts File for a description of the schrodinger.hosts file.