Prime Energy Properties

A Prime energy calculation produces the Prime Energy, and in addition generates individual contributions to the energy of various types, as described in Table 1. These properties are written to Maestro files as Prime properties. Other properties that are derived from the Prime Energy, such as binding energies, are often also broken down into these contributions. Further information on these properties can be found in Reference 3

Table 1. Output energy property types from a Prime calculation.
Property	Description
Coulomb	Coulomb energy
Covalent	Covalent binding energy
vdW	Van der Waals energy
Lipo	Lipophilic energy
Solv GB	Generalized Born electrostatic solvation energy
Energy	Prime energy
Hbond	Hydrogen-bonding correction
Packing	Pi-pi packing correction
SelfCont	Self-contact correction

When a VSGB solvation model is used, the internal dielectric constant for the Coulomb energy is modified on a per-atom basis for charged functional groups. The Coulomb term therefore reflects solvent-influenced electrostatics rather than a pure vacuum Coulomb energy, and the total energy cannot be decomposed into independent vacuum and solvation contributions.

Two versions of the VSGB model are available: VSGB 2.0 (default for OPLS_2005) and VSGB 2.1 (default for OPLS4). Both versions apply the variable dielectric treatment to all charged functional groups in the system, including non-protein molecules. VSGB 2.1 was reparameterized for OPLS4 and includes broader recognition of charged functional groups, particularly in heterocyclic and aromatic systems.