Uses GEMS/GMML to figure out which CYS residues should be bonded to each other based on distance, then writes tleap bonds commands.
You'll need GEMS and GMML. See here for installation instructions: http://glycam.org/docs/gems/download-and-install/.
2017-06-28 you'll need the gmml-dev branch:
git clone -b gmml-dev https://github.com/GLYCAM-Web/gmml.git gmml
export GEMSHOME= # eg: export GEMSHOME=/home/oliver/Programs/gems
qmake
make
You must provide a protein 3D structure
./CYS-bonds protein.pdb
Crashes out if your input file does not exist or you do not provide one, but if you've read this far that shouldn't be happening..