Nonpolar grid-based calculations¶
Parameters for a grid-based nonpolar solvation calculation.
Objects can be initialized with dictionary/JSON/YAML data with the following keys:
calculate energy
: seecalculate_energy()
calculate forces
: seecalculate_forces()
displacement
: finite difference displacement for force calculationgrid spacings
: grid spacings for integral calculation; seegrid_spacings()
molecule
: alias string for molecule to use in calculation; seemolecule()
pressure
: solvent hard sphere pressure; seepressure()
solvent density
: seesolvent_density()
solvent radius
: seesolvent_radius()
surface density
: density of points to use for surface integrals; seesurface_density()
surface method
: method used to calculate the solvent-solute interface; seesurface_method()
surface tension
: seesurface_tension()
temperature
: seetemperature()
APBS apolar calculations follow the very generic framework described in Wagoner JA, Baker NA. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proc Natl Acad Sci USA, 103, 8331-8336, 2006. doi:10.1073/pnas.0600118103.
Nonpolar solvation potentials of mean force (energies) are calculated according to:
and mean nonpolar solvation forces are calculated according to:
In these equations, \(\gamma\) is the repulsive (hard sphere) solvent
surface tension (see surface_tension()
), A is the
conformation-dependent solute surface area (see solvent_radius()
and
surface_method()
), p is the repulsive (hard sphere) solvent
pressure (see pressure()
), V is the conformation-dependent solute
volume (see solvent_radius()
and surface_method()
),
\(\rho\) (see solvent_density()
keywords) is the bulk solvent
density, and the integral involves the attractive portion (defined in a
Weeks-Chandler-Andersen sense) of the Lennard-Jones interactions between
the solute and the solvent integrated over the region of the problem domain
outside the solute volume V. Lennard-Jones parameters are taken from APBS
parameter files as read in through an APBS input file READ statement (see
Data loading input file section (required)).
Note
The above expressions can easily be reduced to simpler apolar solvation formalisms by setting one or more of the coefficients to zero through the keywords.
Warning
All APOLAR calculations require a parameter file which contains Lennard-Jones radius and well-depth parameters for all the atoms in the solute PDB. This parameter file must also contain radius and well-depth parameters for water (specifically: residue “WAT” and atom “OW”). Complete parameter files for protein and nucleic acid parameters are not currently available; we prefer geometric flow calculations (coupled polar and apolar components) rather than this model.
-
apbs.input_file.calculate.nonpolar.Nonpolar.
calculate_energy
¶ Indicate whether energy should be calculated.
Raises: TypeError – if not Boolean
-
apbs.input_file.calculate.nonpolar.Nonpolar.
calculate_forces
¶ Indicate whether forces should be calculated.
Raises: TypeError – if not Boolean
-
apbs.input_file.calculate.nonpolar.Nonpolar.
displacement
¶ Displacement used for finite difference calculation of force.
Units are Å.
Raises: ValueError – if not a number greater than zero
-
apbs.input_file.calculate.nonpolar.Nonpolar.
grid_spacings
¶ Grid spacings for integral quadrature.
Units are Å.
Raises: ValueError – if not a 3-tuple with elements greater than zero
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apbs.input_file.calculate.nonpolar.Nonpolar.
molecule
¶ Alias for molecule to be used in calculation.
Raises: TypeError – if alias is not string.
-
apbs.input_file.calculate.nonpolar.Nonpolar.
pressure
¶ Hard-sphere pressure for solvent in kJ mol-1 Å-3.
This coefficient multiplies the volume term of the apolar model and can be set to zero to eliminate volume contributions to the apolar solvation calculation.
See the documentation for a discussion of units for this property.
Raises: ValueError – if not a non-negative number
-
apbs.input_file.calculate.nonpolar.Nonpolar.
solvent_density
¶ Bulk solvent density.
A floating point number giving the bulk solvent density in Å-3
This coefficient multiplies the integral term of the apolar model discussed above and can be set to zero to eliminate integral contributions to the apolar solvation calculation.
Raises: ValueError – if value is not a non-negative number
-
apbs.input_file.calculate.nonpolar.Nonpolar.
solvent_radius
¶ Radius of the solvent molecules.
This parameter is used to define various solvent-related surfaces and volumes (see
surface_method()
). This value is usually set to 1.4 Å for a water-like molecular surface and set to 0 Å for a van der Waals surface.Raises: ValueError – if value is not a non-negative number
-
apbs.input_file.calculate.nonpolar.Nonpolar.
surface_density
¶ Number of quadrature points per area on surface.
Units are number per Å2 and are used in calculation of surface terms (e.g., molecular surface, solvent accessible surface). This keyword is ignored when
surface_radius()
is 0.0 (e.g., for van der Waals surfaces) or ifsurface method()
refers to splines.A typical value is 10.0.
Raises: ValueError – if value is not a positive number
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apbs.input_file.calculate.nonpolar.Nonpolar.
surface_method
¶ Specifies the model used to construct the solvent-related surface and volume.
This is a string with a value of:
solvent-accessible
: solvent-accessible (also called- “probe-inflated”) surface and volume. See Connolly ML, J Appl Crystallography 16 548-558, 1983 (10.1107/S0021889883010985).
Raises: - ValueError – if surface method is not a valid value
- TypeError – if surface method is not a string
-
apbs.input_file.calculate.nonpolar.Nonpolar.
surface_tension
¶ Surface tension coefficient for apolar solvation models.
The value is a floating point number designating the surface tension in units of kJ mol-1 Å-2. This term can be set to zero to eliminate the SASA contributions to the apolar solvation calculations.
See the documentation for a discussion of units for this property.
Raises: ValueError – if not a non-negative number
-
apbs.input_file.calculate.nonpolar.Nonpolar.
temperature
¶ Temperature for the calculation in Kelvin.
Raises: ValueError – if not a positive number (no violations of the 3rd Law!)