Running Glide from the Command Line

This manual contains information on running Glide from the command line. Although you will usually set up Glide jobs using the controls and settings in the Maestro GUI, you sometimes might want to submit jobs from the command line for the following reasons:

• The command-line scripts can run all full-featured jobs written using the Glide panels in Maestro, and also allow you to override specific run-time values that are not accessible through the Maestro interface.

• Command-line scripts allow you to run Glide jobs when you want.

• Input files and scripts can be modified and jobs can be re-run without reconfiguring and reloading job settings in Maestro.

Using Maestro is the best way to write Glide input files, even if you intend to run them from the command line, because the files are syntactically correct. To create the input files needed to run a job from the command line, set up the job in Maestro, choose Write from the Job Settings button menu , and then modify the files that are generated.

Glide jobs are started with the glide command. This command reads a Glide input file, processes it and runs the executable. You can run both single-processor and distributed Glide docking jobs with this command. The input file can be set up with a script—see glide_sif.py Command Help.

Glide also has some command-line utilities, kept in the utilities subdirectory of the installation, which are described in Glide Utilities.

• For information about general-purpose utilities, see the General Utilities manual.

• For general information about running jobs, see Running Schrödinger Applications from the Command Line. More detailed information can be found in Running Jobs (JOB CONTROL IS DEPRECATED).

An additional related tool is GlideEM, in which ligands are placed in the binding site using a combination of the protein contacts and the electron density. See glideEM.py Command Help for more information.