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 Working Directory options

Choose how the working directory is set when Maestro starts or when a project is opened. Job files are written to the working directory by default. File selectors display the contents of the working directory when first opened.

If you change the working directory explicitly after choosing one of these options, the new directory is used instead. For more information, see Changing the Working Directory.

Specific location option

Set the working directory to a fixed location that does not change with the project.

• Maestro default—Use the standard OS-specific directory. On Linux, this is the directory from which Maestro was started. On Windows and Mac, this is the Schrodinger folder in your Documents folder.

• Other—Specify a directory to use. Enter the path in the text box or click Browse to select a directory.

Location depends on project option

Set the working directory to a location relative to the active project. The working directory changes when a different project is opened.

• Same location as project—Set the working directory to the parent directory of the current project (the directory that the project is in). For zipped projects, this is the directory that contains the .prjzip file.

• Inside project—Set the working directory to the top-level directory inside the current project (project-name.prj).

• Inside project's jobs directory—Set the working directory to the jobs subdirectory of the current project (project-name.prj/jobs).

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.