Force Field Builder - OPLS4/OPLS5 Panel

Customize torsions that are not explicitly included in the OPLS4 or OPLS5 force field by fitting to quantum-mechanical calculations for a set of molecules.

To open this panel: click the Tasks button and browse to Free Energy Perturbation → Force Field Builder, or click the Customize button in any panel that has tools for setting the force field.

  • Using
  • Features
  • Additional Resources

Using the Force Field Builder - OPLS4/OPLS5 Panel

This panel is designed to provide force-field parameters for torsions that are not explicitly represented in the force field. The set of molecules that is provided is analyzed to locate such torsions, and you can then run quantum-mechanical calculations on these molecules, which are fitted to obtain parameters for the torsions. By default, all torsions that are found are fitted simultaneously, but you can exclude selected torsions from the fit and refit the data.

The torsional energies are calculated by performing coordinate scans with Jaguar, then fitting the resulting energy curves to produce new force-field parameters. These calculations can take a long time. They can be run on multiple processors to decrease the turnaround time.

The custom force field parameters can be used by selecting Use customized version in any application panel that supports OPLS4 or OPLS5. You can also set preferences for the use of the force field and the customized version, so that they are selected by default in the application panels.

For information on running the force-field builder from the command line, see ffbuilder Command Help. Merging new parameters into your custom force field from the command line can be done with custom_params Command Help.

Force Field Builder - OPLS4/OPLS5 Panel Features

Start with project option menu

Choose a Force-Field Builder project that contains output you want to analyze or build on. The menu contains a list of recent projects. The default is None, which indicates the start of a new analysis.

When you choose a project, the structures and fragments from that project, and their data, are loaded into the panel, and replace the contents of the All structures table. You can then add structures to the set imported from the project.

Add structures from option menu

Choose the source of the structures to analyze. If you choose File, a file browser opens, so you can locate and open the file. The structures from the chosen source are added immediately to the All structures table, replacing the structures from the previous source (but not structures loaded from a project). If you choose Workspace or Project Table, the All structures table is updated as you change the Workspace content or the entry selection.

Preview New Missing Torsions button

Analyze new structures for missing torsions and associated fragments. This is necessary before the structures can be selected in the All structures table. The analysis may take some time, and a progress bar is displayed. However, you can run a job on a set of new structures without previewing the missing torsions.

Advanced Options link

Set options for analysis of the structures. Opens a dialog box, in which you can set the following options for fragmenting the molecules:

Do not split ligands into fragments for fitting option

This option controls whether ligands are trimmed down into fragments for fitting, or left as they are. If the ligands you supply are the actual molecules you want to use for fitting, select this option. Otherwise, the molecules will be split into fragments (the default).

Include previously fit torsions option

In the fitting procedure, include previously fit torsions.

Theory for optimization and single point energy options

Specify the level of theory to use for geometry optimizations and single point energy calculations. MPNICE is a Machine Learning Force Field (MLFF) and is the recommended method. To learn more about this method, please see Machine Learning Force Fields.

  • DFT—Optimize structures with Jaguar using DFT.

  • MPNICE—Use the Schrödinger MPNICE MLFF for structures that are composed of the supported elements, DFT for other structures. This is the default.

All structures table

This table shows the 2D structures for all the structures to be analyzed. New structures are grayed out (i.e. cannot be selected) until they have been analyzed for missing torsions using the Preview New Missing Torsions button. You can set the number of columns in the table using the Columns option menu.

You can select a structure to show the fragments used for torsion generation in the fragments table; you can also select a torsion on a structure, and the fragments contributing to that torsion from all structures are shown in the table.

All fragments table

This table shows the analysis of structures into fragments that can be used to generate new parameters. Select a force field from the Display results option menu to show RMSE and Energy data from that force field. If parameters have not been generated for the force field, you can click Run to do so.

The table shows a 2D image of the fragments, with the torsion for parameter generation marked. Checking the Skip column skips the fragment when parameters are generated. The RMSE of the fit and the energy profile for the torsion are also displayed in the table. The Legend below the table identifies the curves in the energy profile. You can switch between the natural torsion (the average of all the torsions about the rotatable bond) angle (defined by the force field builder) and a torsion angle defined in terms of the positions of four atoms (as is done in FEP+) for display of the energy profile, by clicking the Settings (gear) icon to the left of the Legend and choosing the desired definition.

The fragments that are shown depend on the selection in the structures table. If no structures (or all structures) are selected, all fragments are shown, and the table is labeled All fragments. If a structure is selected, fragments are shown for that structure. If a torsion is selected in one of the structures (or in one of the fragments), fragments from all structures that contribute to the torsion are shown.

Ring substructures highlighted in red indicates a ring with one or more unparameterized torsions. They are fit differently from regular torsions.

For new structures, the table has no fragment information until you analyze the structures for missing torsions with the Preview New Missing Torsions button. If you change the structure source with the Add structures from option menu, the fragments in this table for the added structures are discarded.

Hovering over a marked torsion in a fragment shows information on the parameters for this torsion and the fragments that contribute to the parameters.

Save Parameters button

Save the generated parameters to a custom force field. The custom force field is written by default to the opls_dir folder in your User resources directory. You can change the location in the Preferences panel, under Jobs - Force field.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The job name is used to name the Force Field Builder project, which is a zip file collecting the results. When the job finishes, the new project is added to the Start with project option menu.

The Job Settings button opens the Force Field Builder - OPLS4/OPLS5 - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation. It also displays a progress bar for the job.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

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