| APBS 0.4.0 User Guide: Adaptive Poisson-Boltzmann Solver | ||
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This chapter gives an overview of the binaries, tools, etc. distributed as part of the APBS software package. It is organized by directory; later chapters provide a more in-depth description on tools specific to particular applications
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.
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