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Jaguar User’s Guide
Chapter 10: Troubleshooting
Including the jaguar Command in Your Path
The command “jaguar” is actually a short script that finds the appropriate version of Jaguar to run and passes on any relevant options to
the main Jaguar program.
Try entering the command
jaguar help
If the output from this command was a description of how to use the
jaguar command, the person who installed Jaguar has already set
things up for you nicely, and you can skip the rest of this subsection.
Otherwise, if your machine responded with an error message like
jaguar - Command not found
you should still be able to run Jaguar by entering the full path name
for the jaguar command:
homedir/jaguar
where homedir is the SCHRODINGER directory described above.
However, you will make your future life with Jaguar a lot easier if
you either add the directory homedir to your path (by editing your
shell startup file), or copy the homedir/jaguar script into a directory
that is in your path.
Problems Starting the Interface
If, when you try to start the Jaguar interface with the command:
jaguar &
you get an error message that begins:
Error: Couldn’t find a jaguar.hosts file
in your X window, it indicates that Jaguar is unable to locate (or use)
the jaguar.hosts file, which provides various setup information.
Usually, there should be a jaguar.hosts file in Jaguar’s home directory,
which is set by the environment variable SCHRODINGER and
should be something like /scr/SCHRODINGER. First, make sure you
have set SCHRODINGER in your .cshrc or some other profile file.
(See the subsection The SCHRODINGER Environment Variable
above for more information.) Next, from the SCHRODINGER directory, type “ls -l jaguar.hosts” to make sure this file exists and you have
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Section 10.1: Problems Getting Started