sorry I didn’t realise you needed the gmx_lib for the specbonds, I forgot about your previous e-mail, my apologies.
In this case we should probably remove all possible paths other than the one assigned in the gmx_lib variable in the set of available environment variables, so that gromacs is only finding one force field folder. This problem is easy to solve when working in an interactive way, as you can use a number as an input for the force-field selector, but is not the case for the -ff parameter that is the one used by the building block. Just out of curiosity, how did you solve it?
Regarding the Zn coordination, the behaviour of the special bonds is not always easy to follow. I would recommend to take a careful look at the log file of the pdb2gmx tool, and identify if the restraint is applied. A line like this one should appear (similar to the ones appearing for the disulfide bonds):
Linking HID-356 NE2-2891 and ZN2-597 ZN-4863...
If this is not present, then you should try to play with the distance assigned in the specbond file, which if I’m not wrong gromacs is using to try to find an atom within ±10%
of this value, otherwise the bond is not created.
Hope it helps.