Invocation

As mentioned in the Installation intructions, the main APBS binary is installed in ${FETK_PREFIX}/bin/${prefix}/ where ${prefix} is a machine-specific directory. Of course, you can move the binary to any directory you choose. APBS is invoked with a very simple syntax:

apbs input-file

where input-file is an input file with a specific syntax described in the APBS Input File section of this manual. Besides the output files specified in input-file, APBS writes data to three additional places:

• Standard output. This will appear on your screen (if you don't redirect it somewhere) and will contain all the basic information about the electrostatics calculation.

• Standard error. This will also appear on your screen (if you don't redirect it somewher) and will contain warnings and error messages.

• The file io.mc (or io.mc_N for parallel runs, where N is the processor ID. This gives you detailed information about the progress of the run with a particular focus on the numerical solver.