I tried to generate Protein/Nucleic acid - Decoy structures using Rosetta, but failed in the low-resolution docking protocol. It seems to be a similar problem as already mentioned in no-output-pdb-files-after-docking-protein-and-dnarna.
I wanted to reproduce the results of 10.1371/journal.pone.0074443. They used Rosetta for generating decoy structures of protein / nucleic acid complexes. Unfortunately, there was no further information given in the paper that might help me generating the decoys appropriately. I have read about an Rosetta extension for nucleic acid docking 10.1371/journal.pone.0108928, but their "patch-download-link" is dead, so I cannot try.
Can anyone help?
I'll note that when I tried it just now, the link for the patch for 10.1371/journal.pone.0108928 is working, at http://albios.saclay.inria.fr/rosettadockrna