Ligand Docking - Job Settings Dialog Box

The Job Settings dialog box is used to specify settings that are used when starting jobs from Maestro. Settings are stored for each application (with a few exceptions).

To open this dialog box, click the Job Settings button in the Job Toolbar,

or click the arrow next to this button and choose Job Settings.

The features in this dialog box depend on whether Active Learning mode is enabled or disabled in the Ligand Docking Panel.

  • Features
  • Additional Resources

Ligand Docking - Job Settings Dialog Box Features

Output section

This section provides options for handling the output of the job.

Incorporate option menu

Choose the manner in which the structural and property results of the calculation are incorporated into the project. The menu can have one or more of the following options:

Append new entries as a new group

Each structure in the output file is added to the project as a new entry, and the entries are grouped. The group name is set to the name of the file from which the entries were read, minus the extension. This is the default option.

Append new entries in place

Each new entry is added to the project immediately below its source entry, i.e. the entry that was used as input for the job. If there is no source entry, the new entry is added to the end of the entry list in the project as an individual entry.

Replace existing entries

Any entries that served as input for the job are replaced with the new structures returned from the calculation. This option is most useful when the job simply produces properties that are added to the input structure, or where there is a single output structure for each input structure.

Do not incorporate

No change is made to the project when the job is complete. This option is always present on the menu.

The choice that you make from this menu is persistent for a given job type: the next time you run a job of that type, the incorporation mode that you last used is the default mode. The incorporation mode is stored as a preference by Maestro, so the choice persists across Maestro sessions.

Job section (Regular Docking Mode)

This section provides options for controlling the job when Active Learning mode is disabled.

Job text box

Enter a name for the job. Job names cannot contain spaces or nonprinting characters.

When a job is started, a subdirectory of the working directory is created using the job name (depending on the application), for writing job files in. Job files are named with the job name as the first part (stem or prefix) of the file names.

The initial name shown is a standard name for the application, which might include calculation settings. A standard name that contains settings is updated when the settings change. You can modify a standard name; if you do and it still retains some settings, the name is updated if the settings change. You can also replace the entire job name.

When a standard name or modified standard name is used, the job name is made unique by appending an integer. This is done by checking for job directories or files in the current working directory. However, if you replace the job name to create a custom job name, the name might no longer be unique, and it is not automatically made unique. In that case, a warning is posted before any files are overwritten.

After a job is submitted, a new job name is automatically created for the next job from the current job name, by appending an integer or incrementing the integer. This is done for custom job names as well as standard or modified names.

Docking CPU option menu

The Docking CPU menu displays all the hosts defined in the Job Server’s hosts.yml file, with the number of CPUs available on the host in parentheses. To run the selected job on a remote host, choose the host from this menu.

The host localhost means the host on which you are running Maestro. If you run a job locally, Maestro automatically reduces the priority of the job so that it does not compete with Maestro for resources. To change this behavior, set the SCHRODINGER_NICE environment variable (see Job Server Environment Variables).

Total N processors text box

Specify the maximum number of processing units (CPUs) to use to run the job. The maximum number is limited by the number of processing units on the host you choose. The number actually used is limited by the number of licenses available for the type of job, and might vary during the course of the job.

Driver CPU option menu

Choose a host to run the driver on. The menu displays all the hosts defined in the $SCHRODINGER/schrodinger.hosts file, with the number of CPUs or GPUs available on the host in parentheses.

The host localhost means the host on which you are running Maestro. If you run a job locally, Maestro automatically reduces the priority of the job so that it does not compete with Maestro for resources.

This host is optional. Select (None) from the menu if you do not need a separate driver host.

Enable Glide MQ option

Select this option to launch docking jobs with Glide MQ, which distributes the docking work across the available processors to improve throughput. Glide MQ requires that the processors be able to communicate with each other, which is the case for localhost and for supported clusters. This option is selected by default when Docking CPU is set to localhost, and is not selected by default for other hosts.

Customize subjob configuration option and menu

Select this option to control how the docking job is divided into subjobs. Choose one of the following from the menu:

  • Fixed number of subjobs—Split the job into the specified number of subjobs.
  • Max ligands per subjob—Split the job so that each subjob contains no more than the specified number of ligands.

Not available when Enable Glide MQ is selected.

Job section (Active Learning Mode)

When Active Learning is enabled, the job settings dialog box has a different set of host options and does not include subjob settings.

Job name text box

Enter a name for the job. Job names cannot contain spaces or nonprinting characters. The name is used to label the job in the Monitor panel and to name the output files.

Driver CPU option menu

Choose a host to run the driver on. The menu displays all the hosts defined in the $SCHRODINGER/schrodinger.hosts file, with the number of CPUs or GPUs available on the host in parentheses. The host must be available at all times during the job (on-demand).

The host localhost means the host on which you are running Maestro. If you run a job locally, Maestro automatically reduces the priority of the job so that it does not compete with Maestro for resources.

Docking CPU option menu

Choose the CPU host to run the docking subjobs on. This option menu displays all the CPU hosts defined in the $SCHRODINGER/schrodinger.hosts file, with the number of CPUs available on the host in parentheses.

Total N processors text box

Specify the maximum number of processors to use for the docking subjobs.

Evaluation CPU option menu

Displays the host used for evaluation subjobs. This host mirrors the selection made for Docking CPU and cannot be changed independently.

Total N processors text box

Specify the maximum number of processors to use for the evaluation subjobs.

Training GPU option menu

Choose the GPU host to run the training subjobs on. This option menu displays all the GPU hosts defined in the $SCHRODINGER/schrodinger.hosts file, with the number of GPUs available on the host in parentheses. The host must be available at all times during the job (on-demand).

Enable Glide MQ option

Select this option to launch docking jobs with Glide MQ, which distributes the docking work across the available processors to improve throughput. Glide MQ requires that the processors be able to communicate with each other, which is the case for localhost and for supported clusters. This option is selected by default when Docking CPU is set to localhost, and is not selected by default for other hosts.

Action buttons

There are several actions you can take after making settings, by clicking one of these buttons:

  • Run—Save the settings for this job type, and start the current job. If a job requires a GPU host but no GPU host is available in the hosts file, this button is disabled.
  • OK—Save the settings for this job type, but do not start the job.
  • Cancel—Discard the changes made to the settings.

The Help button is also in this set.

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