usemap — APBS-PDB2PQR 1.6 documentation

# usemap

Specify pre-calculated coefficient maps to be used in the Poisson-Boltzmann calculation. These must have been input via an earlier READ statement (see READ input file section).

The syntax for this command is:

    usemap {type} {id}

where the mandatory keywords are:

`type`

  A string that specifies the type of pre-calculated map to be read in:

  `diel`
    Dielectric function map (as read by READ input file section `diel`); this causes the pdie, sdie, srad, swin, and srfm (elec) parameters and the radii of the biomolecular atoms to be ignored when computing dielectric maps for the Poisson-Boltzmann equation. Note that the pdie and sdie values are still used for some boundary condition calculations as specified by bcfl.
  `kappa`
    Mobile ion-accessibility function map (as read by READ input file section `kappa`); this causes the swin and srfm (elec) parameters and the radii of the biomolecular atoms to be ignored when computing mobile ion values for the Poisson-Boltzmann equation. The ion parameter is not ignored and will still be used.
  `charge`
    Charge distribution map (as read by READ input file section `charge`); this causes the chgm parameter and the charges of the biomolecular atoms to be ignored when assembling the fixed charge distribution for the Poisson-Boltzmann equation.
  `pot`
    Potential map (as read by READ input file section `pot`); this option requires setting bcfl to `map`.
`id`
  As described in the READ command documentation (see READ input file section), this integer ID specifies the particular map read in with READ. These IDs are assigned sequentially, starting from 1, and incremented independently for each map type read by APBS. In other words, a calculation that uses two PQR files, one parameter file, three charge maps, and four dielectric maps would have PQR files with IDs 1-2, a parameter file with ID 1, charge maps with IDs 1-3, and dielectric maps with IDs 1-4.