FEP Solubility - Advanced Options Dialog Box

FEP Solubility - Advanced Options Dialog Box Features

• Use Hydration mode only option
• Equilibration time text box
• Hydration time text box
• Sublimation time text box
• OPLS Settings section
  • Force field option menu
    • Use customized version option
    • Parameter set button
  • Generate missing parameters with Force Field Builder option
  • Merge Parameters button
• Reset button

Use Hydration mode only option

Select this option to only perform the hydration (or solvation) simulations. Only the free energy of Hydration is calculated.

Equilibration time text box

Set the time for equilibration of the ligand cluster system, in ns. The equilibration follows a relaxation simulation on the ligand cluster; after the equilibration, the cluster is merged with the solvent to form the initial structure for the sublimation simulations.

Not available if Use Hydration mode only is selected.

Hydration time text box

Specify the time for production simulation of the hydration (or solvation) step, in which a single solvated ligand molecule is removed from the solvent. The values are given in ns.

Sublimation time text box

Specify the time for production simulation of the sublimation step, in which a ligand molecule is removed from the aggregate. The values are given in ns.

Not available if Use Hydration mode only is selected.

OPLS Settings section

Select an option for the source of custom OPLS parameters, and for generating missing parameters. Once selected, the source is used within the current instance of the FEP+ panel until the panel is closed or the source is changed again. The options available depend on your license.

Force field option menu

Choose the force field for the simulations. The choices are OPLS4 or OPLS5. The default is OPLS4, unless you set the default in the Force Field settings section of the Preferences Panel.

Use customized version option

Use your customized version of the OPLS force field, rather than the standard version in the distribution. This option is set by default to the value of the Use custom parameters by default option in the Preferences panel, under Jobs - Force field, when the current panel is opened. The default directory for the customized version can also be specified as a preference, in the same location.

If the customized version is missing or invalid, the text of this option turns orange and an orange warning icon is displayed to the right, with a tooltip about the problem.

Parameter set button

Select the set of custom parameters for the OPLS force field. Opens the Set Custom Parameters Location Dialog Box.

Generate missing parameters with Force Field Builder option

Run the Force Field Builder to generate any missing force-field torsional parameters before running the FEP+ job.

Merge Parameters button

Merge a set of custom force field parameters into the current custom parameters file (defined in the Set Custom Parameters Location Dialog Box, see Force Field settings for information). Opens a file selector in which you can browse to and select the Force Field Builder project (*_ffb.zip) where the custom force field parameters are stored.

This button is only available when you select Use customized version.

Reset button

Reset the dialog box to its default settings, clearing all data. The force field customization is reset to the value set in the Force Field settings section of the Preferences panel.