Well I have run AbinitioRelax.linuxgccrelease for the first time and had it produce a t000_silent.out file. The documentation says to use score.linuxgccrelease but that no longer exists in rosetta 3.2. What do I need to do to get .pdb files from the silent output file? Thanks.
Silent files are such a pain.
Try score_jd2 or extract_pdbs. (I think the sole purpose of extract_pdbs is this).
Thanks, I tried extract_pdbs and that worked.