A collection of hacked-together useful scripts to mitigate the pain of preparing systems with Gromacs 4.0.*.
This will not solve all your problems, but may help by giving you a starting point when trouble shooting GMX 4.0 system preparation.
Take a look at the 'prepare-gmx40.sh' script for an example workflow.
In order to run you need the 'pdb2gmx' (from gromacs) and 'tleap' (from ambertools) in your PATH. You need Python 2.7 to for the python scripts.