OPLS Virtual Sites

forcefield

Virtual sites are partial charges placed at positions away from atomic centers. They improve the accuracy of electrostatic interactions for functional groups whose charge distributions cannot be represented well by atom-centered charges alone. Both the OPLS4 and OPLS5 force fields use virtual sites.

Virtual sites are distinct from the default partial charges displayed in Maestro. To inspect the virtual sites assigned by a given OPLS force field, you must generate them explicitly using the ffld_server utility as described below.

Virtual Sites in OPLS4

OPLS4 uses off-atom-centered virtual sites for functional groups with significant anisotropic nonbonded interactions. These are static charge sites whose positions are determined by the local molecular geometry.

Sulfur—Virtual sites represent lone-pair and sigma-hole charge distributions on sulfur-containing moieties including thiols, sulfides, disulfides, and aromatic sulfur (e.g., thiophene). These sites improve the representation of chalcogen bonds with oxygen and nitrogen.
Halogens—Virtual sites on bromine and iodine atoms represent sigma-hole charge distributions, improving the directionality of halogen bond interactions.
Aromatic nitrogen—Virtual sites represent the lone-pair charge distribution of nitrogen atoms in aromatic heterocycles.

Virtual Sites in OPLS5

OPLS5 retains all virtual sites from OPLS4 and adds two types of additional off-center charge sites.

Drude oscillators—Classical Drude oscillators on select functional groups model induced polarization. Each Drude oscillator is a mobile point charge connected to its parent atom by a harmonic spring. The mobile charge relaxes to its energy minimum for each configuration, allowing the electrostatic model to respond to the local environment. This improves the accuracy of cation-pi interactions and hydrogen bonds involving charged species.
Fluctuating charge transfer (FlucCT) sites—For transition metal complexes, a fluctuating charge model dynamically redistributes charge between metal centers and coordinating ligands. This is combined with Morse potential and angular overlap model (AOM) terms for improved metal-ligand geometry.

Visualizing Virtual Sites

You can generate structures that include virtual site positions and charges using the ffld_server utility with the -save_virt option. The output file includes virtual sites as additional atoms that can be viewed in Maestro.

Note: Output files that contain virtual sites are suitable for visualization only. Do not use them as input for further calculations.

General Workflow

To visualize the virtual sites assigned to a structure by a specific OPLS force field, run the following command:

On Linux or macOS:

$SCHRODINGER/utilities/ffld_server -version N -imae input.maegz -omae output.maegz -save_virt

On Windows, open the Schrödinger Command Prompt or Schrödinger Power Shell:

ffld_server -version N -imae input.maegz -omae output.maegz -save_virt

The -version flag specifies the force field:

Version flag	Force field
`-version 16`	OPLS4
`-version 17`	OPLS5
`-version 14`	OPLS_2005

The -save_virt option writes virtual sites as additional particles in the output file. Open the output file in Maestro to view the virtual site positions.

FEP+ Partial Charge Workflow

The partial charges used in Desmond and FEP+ calculations are molecule-specific custom charges that differ from the default charges displayed in Maestro. To visualize the charges and virtual sites used in an FEP+ calculation, run two commands in sequence: