edu.duke.cs.osprey/edu.duke.cs.osprey.gui.forcefield.amber/AmberForcefieldParams

AmberForcefieldParams

abstract class AmberForcefieldParams(ffnameOverrides: Map<MoleculeType, ForcefieldName>) : ForcefieldParams

Types

inner class AtomPairParams(esQ: Double, vdwA: Double, vdwB: Double) : ForcefieldParams.AtomPairParams

inner class AtomPairsParams(top: AmberTopology.Mapped, indexToTop: Map<Int, Map<Int, Int>>) : ForcefieldParams.AtomPairsParams

AtomParams

class AtomParams(type: String, charge: String) : ForcefieldParams.AtomParams

AtomsParams

class AtomsParams(types: AmberTypes, frcmods: List<String>) : ForcefieldParams.AtomsParams

Functions

combineAtomsParams

open override fun combineAtomsParams(info1: ForcefieldParams.AtomsInfo, info2: ForcefieldParams.AtomsInfo): ForcefieldParams.AtomsParams

Combines together atoms params from two variations of the same molecule. Useful for eg applying two mutations to the same molecule. If the two atoms parameters disagree on params for an atom, the tie should be broken by picking the atom params from the atoms params whose given atom indices contain the disagreeable atom's index. The two given sets of atom indices should not overlap. If a tie can't be broken with the preferred atom indices, the implementation should throw an exception.

parameterizeAtomPairs

open suspend override fun parameterizeAtomPairs(infos: List<ForcefieldParams.MolInfo>): AmberForcefieldParams.AtomPairsParams

Compute the forcefield parameters for a list of molecules.

parameterizeAtoms

open suspend override fun parameterizeAtoms(mol: Molecule, atomIndex: AtomIndex, netCharge: Int?): AmberForcefieldParams.AtomsParams

Compute the forcefield parameters for a molecule.

settings

open override fun settings(): LinkedHashMap<String, Any>

Any settings needed by the Osprey runtime to calculate this forcefield.

Properties

chargeMethod

var chargeMethod: AmberChargeMethod

Method to generate partial charges for small molecules.

dielectric

var dielectric: Double

The dielectric constant of the environment (aka its relative permittivity), which influences electrostatic calculations.

distanceDependentDielectric

var distanceDependentDielectric: Boolean

If true, multiply the dielectric contstant by the atom pair distance (r) for electrostatic interactions.

ffnameOverrides

val ffnameOverrides: Map<MoleculeType, ForcefieldName>

forcefield

abstract val forcefield: Forcefield

sqmMinimizationSteps

var sqmMinimizationSteps: Int = 0

Number of steps of xmin minimization to perform during partial charge calculation for small molecules.

unconnectedDistance

open override val unconnectedDistance: Int = 5

What's the smallest bond distance where two atoms are treated the same as two totally unconnected atoms? eg. 1-4 bonds should use 4, 1-5 bonds should use 5

vdwScale

var vdwScale: Double

Scaling to apply to the van der Waals calculations.

Inheritors

Amber96Params

Amber14SBParams