For detailed information on how to use APBS please see APBS documentation and APBS tutorial.
In additions to tools available in /opt/apbs/tools directory you may find very useful the PDB2PQR web service which vastly simplifies preparation of APBS input files. Command line version of this utility is available in /opt/apbs/pdb2pqr as pdb2pqr.py.
For additional help there are two APBS maling lists: apbs-users and apbs-announce. The list archives are excellent source in case you have any problems using APBS.