OEPotentialTerms¶
This namespace contains constants describing potential terms which might be calculated
in different Szybki runs. Entries: OEPotentialTerms_VdW,
OEPotentialTerms_Coulomb, OEPotentialTerms_Bond,
OEPotentialTerms_Bend, OEPotentialTerms_StretchBend,
OEPotentialTerms_Torsion and
OEPotentialTerms_ImproperTorsion
correspond to the total MMFF94 or Smirnoff potential terms.
In the case of partial optimization of the protein, entries with a prefix Ligand refer to
the force field terms of the ligand (for example OEPotentialTerms_LigandVdW),
while entries with a prefix Protein (for example OEPotentialTerms_ProteinVdW)
are for the MMFF94 or Smirnoff terms of the flexible part of the protein.
Force field terms describing VdW and Coulomb interactions between the ligand and the flexible part of
the protein are defined with the constants OEPotentialTerms_ProteinLigandVdW
and OEPotentialTerms_ProteinLigandCoulomb respectively.
Term OEPotentialTerms_ProteinLigandInteraction describes complete ligand-protein
interaction according to the protein electrostatic model chosen.
Values defined by OEPotentialTerms_SheffieldSolvation,
OEPotentialTerms_PBSolvation and OEPotentialTerms_CavitySolvation
refer to solvation energies used to optimize a ligand in solution, while the term
OEPotentialTerms_HarmonicConstraint determines the he value of the imposed harmonic
constraint. Entries: OEPotentialTerms_VdWProteinLigand,
OEPotentialTerms_CoulombProteinLigand,
OEPotentialTerms_ProteinDesolvation,
OEPotentialTerms_LigandDesolvation, OEPotentialTerms_SolventScreening,
OEPotentialTerms_GridCoulomb and OEPotentialTerms_ExactCoulomb are
used to break down the total protein-ligand interaction energy into components.
Value of the OEPotentialTerms_ProteinPseudoLigandInteraction represents
the interaction of the flexible part of of the optimized protein-ligand system (ligand + flexible part
of the protein) with the rest of the protein and as such is not an observable quantity.
When Amber force field is applied for protein-ligand interaction, values of
OEPotentialTerms_ProteinLigandAmberVdW and
OEPotentialTerms_ProteinLigandAmberCoulomb are used for the corresponding vdW and
Coulomb protein-ligand energies. Term OEPotentialTerms_TorsionHarmonicConstraint
is the value of the constraint torsion harmonic potential. Two terms:
OEPotentialTerms_IEFFInteraction and OEPotentialTerms_InterLigandIEFF
are IEFF energies, total and interligand respectively. The latter has nonzero value when more than one
ligand are present in the active site of the protein.
VdW
Value of vdW energy
Coulomb
Value of Coulomb energy
Bond
Value of bond stretch energy
Bend
Value of angle bend energy
StretchBend
Value of stretch-bend energy. This potential term appears only when MMFF force field is used
Torsion
Value of torsion energy
ImproperTorsion
Value of improper torsion energy
LigandVdW
Value of ligand vdW energy
LigandCoulomb
Value of ligand Coulomb energy
LigandBond
Value of ligand bond energy
LigandBend
Value of ligand angle bend energy
LigandStretchBend
Value of ligand stretch-bend energy. This potential term appears only when MMFF force field is used
LigandTorsion
Value of ligand torsion energy
LigandImproperTorsion
Value of ligand improper torsion energy
ProteinVdW
Value of protein vdW energy
ProteinCoulomb
Value of protein Coulomb energy
ProteinBond
Value of protein bond energy
ProteinBend
Value of protein angle bend energy
ProteinStretchBend
Value of protein stretch-bend energy. This potential term appears only when MMFF force field is used
ProteinTorsion
Value of protein torsion energy
ProteinImproperTorsion
Value of protein improper torsion energy
ProteinLigandVdW
Value of protein-ligand vdW energy
ProteinLigandCoulomb
Value of protein-ligand Coulomb energy
ProteinLigandInteraction
Value of total protein-ligand interaction
SheffieldSolvation
Value of Sheffield solvation energy
HarmonicConstraint
Value of atom harmonic constraint energy
PBSolvation
Value of PB solvation energy
CavitySolvation
Value of cavity solvation energy
VdWProteinLigand
Value of protein-ligand vdW interaction energy
CoulombProteinLigand
Value of protein-ligand Coulomb interaction energy
ProteinDesolvation
Value of protein desolvation energy
LigandDesolvation
Value of ligand desolvation energy
SolventScreening
Value of PB solvent screening energy
GridCoulomb
Value of protein-ligand Coulomb energy on grid
ExactCoulomb
Value of exact protein-ligand Coulomb energy
ProteinPseudoLigandInteraction
Value of ligand and flexible protein (pseudoligand) interaction with the rest of the protein energy
ProteinLigandAmberVdW
Value of Amber protein-ligand vdW energy
ProteinLigandAmberCoulomb
Value of Amber protein-ligand Coulomb energy
TorsionHarmonicConstraint
Value of torsion harmonic constraint energy
IEFFInteraction
Value of total IEFF intermolecular energy
InterLigandIEFF
Value of interligand IEFF energy
Max
Number of potential terms