READ input file section — APBS-PDB2PQR 1.6 documentation

# READ input file section

The READ block of an APBS input file has the following general format:

    READ
        [ keywords... ]
    END

where `keywords` is or more of the keywords described below (the line breaks and indentation are for clarity; only whitespace is necessary).

Note

One of these sections must be present for every molecule involved in the APBS calculation. Molecule and “map” IDs are assigned implicitly assigned for each molecule/map read, based on order and starting at 1 and incremented independently for each input type. In other words, each input PQR file is assigned an ID 1, 2, 3, …; each input dielectric map is assigned an independent ID 1, 2, 3, …; etc.

## charge

This command allows APBS to read the fixed (molecular) charge density function mapped to a mesh. The inputs are maps of charge densities; these values have units of ec Å-3, where ec is the electron charge. In general, this command will read charge-maps written by ELEC input file section write commands. The syntax of this command is:

    READ charge {format} {path} END

`format`

  Specify the format of the charge map. Acceptable values include:

  `dx`
    OpenDX scalar data format
  `gz`
    gzipped (zlib) compressed OpenDX scalar data format. Files can be read directly in compressed form.
`path`
  The location of the charge map file.

## diel

This command allows APBS to read the dielectric function mapped to 3 meshes shifted by one-half grid spacing in the x, y, and z directions. The inputs are maps of dielectric variables between the solvent and biomolecular dielectric constants; these values are unitless. In general, this command will read dielectric maps written by by ELEC input file section write commands. The syntax of this command is:

    READ diel {format} {path-x} {path-y} {path-z} END

`format`

  The format of the dielectric map.

  `dx`
    OpenDX scalar data format
  `gz`
    gzipped (zlib) compressed OpenDX scalar data format. Files can be read directly in compressed form.
`path-x`
  The location of the x-shifted dielectric map file.
`path-y`
  The location of the y-shifted dielectric map file.

`path-z` The location of the z-shifted dielectric map file.

Note

If you choose this option and have a non-zero ionic strength, you must also include a READ kappa statement.

## kappa

This command allows APBS to read the ion-accessibility function mapped to a mesh. The inputs are maps of ion accessibility values which range between 0 and the build Debye-Hückel screening parameter; these values have units of Å-2. In general, this command will read kappa-maps written by by ELEC input file section write commands. The syntax of this command is:

    READ kappa {format} {path} END

`format`

  Specify the format of the charge map. Acceptable values include:

  `dx`
    OpenDX scalar data format
  `gz`
    gzipped (zlib) compressed OpenDX scalar data format. Files can be read directly in compressed form.
`path`
  The location of the map file.

Note

If you choose this option, you must also include a read diel statement.

## mol

This command specifies the molecular data to be read into APBS. The syntax is

    READ mol {format} {path} END

`format`

  The format of the input data.

  `pqr`
    Specify that molecular data is in PQR format.
  `pdb`
    Specify that molecular data is in pseudo-PDB format. If this type of structure file is used, then a parameter file must also be specified with a READ parm statement to provide charge and radius parameters for the biomolecule’s atoms.
`path`
  The location of the molecular data file.

## parm

This command specifies the charge and radius data to be used with pseudo-PDB-format molecule files. The syntax is:

    READ parm {format} {path} END

`format`

  The format of the parameter file.

  `flat`
    Specify that the parameter file is in APBS flat-file parameter format.
  `xml`
    Specify that the parameter file is in APBS XML parameter format
`path`
  The location of the parameter data file.

Note

APBS provides a few example files as part of the source code distribution. Currently, example files only contain the polar parameters that can also be assigned more easily through the PDB2PQR software.

## pot

This command allows APBS to read the electrostatic potential mapped to a mesh. The inputs are maps of the electrostatic potential from a previous calculation. In general, this command will read potential-maps written by by ELEC input file section write commands. The syntax of this command is:

    READ pot {format} {path} END

`format`

  Specify the format of the charge map. Acceptable values include:

  `dx`
    OpenDX scalar data format
  `gz`
    gzipped (zlib) compressed OpenDX scalar data format. Files can be read directly in compressed form.
`path`
  The location of the map file.

Note

To use this functionality you must set the bcfl keyword to `map`. See also: usemap.