Solvation methods
[Molecular Modeling]

This chapter contains all relevant information on the use of BALL solvation methods. More...

Collaboration diagram for Solvation methods:

Classes
class	BALL::ClaverieParameter
	ClaverieParameter class. More...
class	BALL::ElectrostaticPotentialCalculator
	This class is used to compute the electrostatic potential for of a system. More...
class	BALL::Pair6_12InteractionEnergyProcessor
	Processor for the computation of the van-der-Waals interaction energy of a molecule with its surrounding. More...
class	BALL::Pair6_12RDFIntegrator
	6-12 pair potential integrator. More...
class	BALL::PairExpInteractionEnergyProcessor
	Processor for the computation of the van-derWaals interaction energy of a molecule. More...
class	BALL::PairExpRDFIntegrator
	6-exp pair potential integrator. More...
class	BALL::PCMCavFreeEnergyProcessor
	Processor for the computation of the cavitation free energy. More...
class	BALL::PierottiCavFreeEnergyProcessor
	Processor for the computation of the cavitation free energy. More...
class	BALL::FDPB
	Finite Difference Poisson Boltzmann Solver. More...
class	BALL::ReissCavFreeEnergyProcessor
	Processor for the computation of the cavitation free energy. More...
class	BALL::SolventAtomDescriptor
	This struct contains the information for one atom type of the solvent. More...
class	BALL::SolventDescriptor
	Solvent Description. More...
class	BALL::SolventParameter
	Parameter section for the solvent description. More...
class	BALL::UhligCavFreeEnergyProcessor
	Processor for the computation of the cavitation free energy. More...
Functions
BALL_EXPORT TRegularData3D < char > *	BALL::calculateSESGrid (const Vector3 &lower, const Vector3 &upper, float spacing, const System &system, float probe_radius)
	calculateSESGrid
BALL_EXPORT TRegularData3D < char > *	BALL::calculateSASGrid (const Vector3 &lower, const Vector3 &upper, float spacing, const System &system, float probe_radius)
	calculateSASGrid
BALL_EXPORT double	BALL::calculateOoiEnergy (AtomContainer &atoms)
	Calculate the solvation energy after Ooi et al.

---

Detailed Description

This chapter contains all relevant information on the use of BALL solvation methods.

---

Function Documentation

BALL_EXPORT double BALL::calculateOoiEnergy

(

AtomContainer &

atoms

)

Calculate the solvation energy after Ooi et al.

This function computes the solvation energy using the empirical surface model proposed by Ooi et al.(T. Ooi, M. Oobatake, G. Nemethy, H. A. Scheraga: Accessible surface areas as a measure off the thermodynamic parameters of hydration of peptides, Proc. Natl. Acad. Sci. USA, Vol. 84 (1987), pp. 3086-3090).

The method is parameterized for proteins only. Calling the function with different structures probably yields results of arbitrary meaninglessness.

The energy is returned in units of kJ/mol. Unparametrized atoms are simply ignored, which might lead to unreasonable values.

Files:

types and parameters are taken from data/solvation/Ooi.ini