Recent site activity

APBS‎ > ‎User guide‎ > ‎Running APBS‎ > ‎Input files‎ > ‎ELEC input file section‎ > ‎ELEC keywords‎ > ‎

usemap

Specify pre-calculated coefficient maps to be used in the Poisson-Boltzmann calculation. These must have been input via an earlier READ statement. The syntax 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 diel); this causes the pdie, sdie, srad, swin, and srfm 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 kappa); this causes the swin and srfm 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 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 pot); this option requires setting bcfl to map.  NOTE:  this functionality is only available in the current developmental release of APBS.
id
As described in the READ command documentation, 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.
Comments