File formats
This section introduces some of the input and output file formats which are used by APBS.
PQR biomolecular structure format
The PQR format is the primary input format for biomolecular structure in APBS package. This format is a modification of the PDB format which allows users to add charge and radius parameters to existing PDB data while keeping it in a format amenable to visualization with standard molecular graphics programs. The origins of the PQR format are somewhat uncretain, but has been used by several computational biology software programs, including MEAD and AutoDock. UHBD uses a very similar format called QCD.
APBS reads very loosely-formatted PQR files: all fields are whitespace-delimited, thereby allowing coordinates which are larger/smaller than ± 999 Å.
 | The "cost" of this looser formatting is the inability of APBS to parse PQR files with chain IDs. These fields need to be removed from PQR files before they are used with APBS. |
APBS reads data on a per-line basis from PQR files using the following format:
Field_name Atom_number Atom_name Residue_name Residue_number X Y Z Charge Radius
- Field_name
A string which specifies the type of PQR entry and should either be ATOM or HETATM in order to be parsed by APBS.
- Atom_number
An integer which provides the atom index.
- Atom_name
A string which provides the atom name.
- Residue_name
A string which provides the residue name.
- Residue_number
An integer which provides the residue index.
- X Y Z
3 floats which provide the atomic coordiantes.
- Charge
A float which provides the atomic charge (in electrons).
- Radius
A float which provides the atomic radius (in Å).