In case you get an error message of the form
FATAL ERROR: Setting parameter binaryoutput from script failed!
you should try moving the line specifying the parameter in question in your config file. In particular, the parameter has to preceed any command actually performing calculations. For example, this config file will fail, as binaryoutput comes after minimize which starts the conjuate gradients minimization.
coordinates molecule.pdb structure molecule.psf cutoff 12 exclude scaled1-4 outputname molecule paraTypeCharmm On parameters /home/f/toppar/par_all35_ethers.prm parameters custom.prm temperature 298 switchdist 10 minimization on minimize 1000 binaryoutput no