Jobs Preferences

These settings affect how and where jobs are run and results are saved.

Warn about use of unprepared proteins

Proteins that have been prepared by the Protein Preparation Wizard from Suite 2012 on are marked with a Maestro property. When you start a job with a protein that does not have this property, a dialog box is posted to warn you that the protein does not appear to have been prepared. You can choose to continue and mark the protein as prepared, or cancel the job. Proteins prepared with the Protein Preparation Wizard in releases prior to Suite 2012 do not have this property, and will be regarded as possibly unprepared.

To prevent the display of this dialog box, deselect this option. Proteins will then be accepted regardless of their preparation, but will not be marked as prepared.

Warn before overwriting existing job files

Display a warning dialog box when a job is started or its files written with the same name as an existing job. If the job is run with the same name, the existing job files are overwritten. Deselect this option if you want to overwrite files from existing jobs without displaying a warning. If the existing job is still running, the files will not be overwritten, regardless of this setting, and a warning is displayed.

Use web server for BLAST searches

Use the BLAST web site to perform a BLAST search. This option allows you to run Prime Structure Prediction without having a local copy of the BLAST database. If your query structures are proprietary, you should not select this option.

Use new Glide for docking (faster)

Enabled by default, this option activates the new Glide backend. If disabled, the job will revert to using the traditional Glide backend.

Always run job driver script on remote host

When running jobs on a remote host, run the driver for that job on the remote host as well. This option is useful if you are running on the Cloud, as the driver must run on the remote host. Note that some jobs, such as Glide, Prime MM-GBSA, and Induced Fit Docking, rely on the driver running locally and using the local file system (-LOCAL) to ensure that jobs are restartable. Running these jobs on the remote host will prevent restarting.

Not available if you are using Job Server.

Default directory for job startup and file i/o options

When you choose any of the options below, the current working directory is set to the specified location, and the option you select is stored as a preference. The current working directory is set to the specified location the next time you start Maestro.

Job files are written by default to the current working directory. File selectors display the contents of the current working directory when they are first opened in a Maestro session. Subsequently each file selector stores the last location you visted, and displays the files in that location when you open it again.

Thus, these options set the default by changing the current working directory immediately, on Maestro startup, and when a project is opened if the option is project-related.

If you change the current working directory explicitly after choosing one of these options, the new directory is used as the location for job files and the initial location for file selectors, rather than the choice you make from this set of options. For more information on changing the current working directory, see Changing the Working Directory.

In the descriptions below, the directory is called the default directory.

Note: If you choose an option for a directory that is inside the project, you should wait until any jobs launched from that project finish before you rename the project, or save the project if it is a scratch project.

• Maestro's current working directory—Set the current directory to Maestro's initial working directory. When Maestro starts, this directory on Linux is the directory from which Maestro was started; on Windows and Mac it is the Schrodinger folder in your Documents folder.

• Parent of project directory—Set the current working directory to the parent directory of the current project (the directory that the project is in). Opening a different project or closing a project (which opens a scratch project) sets the current working directory again. For zipped projects, the parent directory is the directory that contains the .prjzip file, rather than the temporary directory into which the zipped project is extracted. This is the default setting for the Materials Science profile.

  Jobs running with this setting are not lost if the project is renamed.

• Project directory—Set the current working directory to the top-level directory inside the current project. This is the project-name.prj directory. This directory changes when a new project is loaded, and the current working directory is reset to the new project directory.

  Jobs running in this directory will fail if the project is renamed. This includes saving scratch projects.

• Project jobs directory—Set the current working directory to the project's jobs subdirectory (project-name.prj/jobs). This directory changes when a new project is loaded or when a scratch project is opened, and the current working directory is reset to the new jobs directory.

  Jobs running in this directory will fail if the project is renamed. This includes saving scratch projects.

• Other (specify below)—Use the specified directory as the current working directory. When using this option, you must enter the desired directory name in the Directory text box.

Copy archived job directory to the launch directory when job finishes (-SAVE) option

When a job finishes, create a zip file of the temporary directory that the job used to write files needed for the job (the job directory), and copy it back to the job launch directory. The zip file is not automatically unzipped. This option can be useful if you need to debug a job that fails, and keep the files, or to use the files for some other purpose. Normally, these files ("scratch files") are deleted and the directory is removed when the job finishes.

This option sends the -SAVE option to Job Control. It is not saved across Maestro sessions, but it is initialized from the SCHRODINGER_SAVE_JOBDIR environment variable.

Run the job in the launch directory and keep all files (-LOCAL) option

When a job is run, use the launch directory as the temporary location to write files needed for the job, and leave the files in place when the job finishes. If the job launches subjobs, the subjobs might not use this directory for their working directory: the behavior depends on the application. If the subjobs do not write to the launch directory, you can set the Copy archived job directory to the launch directory when job finishes option to copy back the subjob temporary directories. Note that in this case, the files that are local already are not archived in a zip file.

This option sends the -LOCAL option to Job Control. It is not saved across Maestro sessions.

Not available if you are using Job Server.

Enable job debug output (-DDEBUG)

When the job is run, print debugging output. This option is useful when running jobs for analysis by Schrödinger technical support. It is not stored between Maestro sessions.

These settings affect the force field that is used by default for jobs that require a force field.

Force field option menu

Choose the OPLS force field that is shown by default on Force field option menus, and is thus the one that is chosen by default for jobs. The choices are OPLS_2005, OPLS4, and OPLS5/OPLS4. OPLS4 is the default force field if you have a license for it, otherwise it is OPLS_2005. If you select OPLS5/OPLS4, panels which support OPLS5 defaults to it, and panels which do not support OPLS5 uses OPLS4.

Customization settings section

When using the OPLS4 or OPLS5 force field, you can choose the standard version or a customized version. These settings allow you to choose which customized version to use by default, and where custom parameters are located. The default version specified here is used if the project does not have a custom parameter set specified.

Location of saved custom parameters option menu

Choose the directory that you want to use for storing and loading custom force-field parameters. The current default is displayed on the menu. Recent choices made for the global default are listed below it. You can set the location for a project in the Set Custom Parameters Location Dialog Box.

To add a custom path, choose Browse and navigate to the desired location in the Custom Parameters Location directory selector.

If a custom force field is used for an MD simulation, the location of the force field is determined at run time from these settings or the settings made for the project. This force field could be different from the one that is in effect when you built the model system for the simulation (including model systems built prior to the 2020-3 release that contain a path to a custom force field).

Reset link

Reset the custom parameters location to the default. The default location in your User resources directory is displayed on the Location of saved custom parameters option menu. Only available when a nondefault location is selected.

Use custom parameters by default option

When choosing OPLS4 or OPLS5 as the force field, use their respective custom parameters by default, rather than the standard parameters. Changing this option sets the Use customized version option in any panel that has access to OPLS4 or OPLS5.

Click here link

Opens the Set Custom Parameters Location Dialog Box so you can set a custom location.