Hi many thanks for helping me out..
I checked on the file permissions..they seem to be fine. Besides, I had no trouble running protein design, ligand and protein docking previously, with the modified files copied from the demos folders..
Here is how I usually run things:
/usr/local/rosetta3.2/rosetta_source/bin/enzyme_design.linuxgccrelease -database /usr/local/rosetta3.2/rosetta_database/ @flags > enzdes.log
The input, flags, params and cst files are all in the folder /usr/local/rosetta3.2/my_file/….
I will try it again by shifting files around after my finals. Thanks for the help!