APOLAR input file section — APBS-PDB2PQR 1.6 documentation

# APOLAR input file section

This section is the main component for apolar solvation calculations in APBS runs. There may be several APOLAR sections, operating on different molecules or using different parameters for multiple runs on the same molecule. The syntax of this section is:

    APOLAR [name id]
      <keywords...>
    END

The first (optional) argument is:

    name <id>

where `id` is a unique string which can be assigned to the calculation to facilitate later operations (particularly in the PRINT input file section statements). The `keywords...` describing the parameters of the apolar calculation are discussed in more detail below:

APOLAR keywords:

- bconc
- calcenergy
- calcforce
- dpos
- gamma
- grid
- mol
- press
- sdens
- srad
- srfm (apolar)
- swin
- temp

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:

\[{W}^{(\mathrm{np})}(x) = \gamma A(x) + pV(x) + \bar \rho \sum^N_{i=1} \int _{\Omega} u_i^{(\mathrm{att})} (x_i, y) \theta (x,y) \, \mathrm{d}y\]

and mean nonpolar solvation forces are calculated according to:

\[\mathbf{F}_i^{(\mathrm{np})}(x) = -\gamma \frac{\partial A (x)}{\partial x_i} - p \int _{\Gamma _i (x)} \frac{y-x_i}{\lVert y - x_i \rVert} \, \mathrm{d}y - \bar \rho \sum _{i=1}^N \int _{\Omega} \frac{\partial u_i^{(\mathrm{att})}(x_i,y)}{\partial x_i} \theta (x,y) \, \mathrm{d}y\]

In these equations, \(\gamma\) is the repulsive (hard sphere) solvent surface tension (see gamma), A is the conformation-dependent solute surface area (see srad and srfm (apolar) keywords), p is the repulsive (hard sphere) solvent pressure (see press keyword), V is the conformation-dependent solute volume (see srad and srfm (apolar) keywords), \(\rho\) (see bconc 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 READ input file section).

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.