Reply To: flexpepdock flag “-packing:unboundrot”

[Anonymous]

If it’s not in the manual, your best bets are asking here, emailing the authors, or reading the code. You can also do -help on Rosetta; here it will tell you something like “core::options::OptionKeys::packing::unboundrot, “Read ‘native’ rotamers from supplied PDB(s). Unlike -use_input_sc, these rotamers will not be lost during repacks. This option requires specific support from the protocol; it is NOT built in to PackerTask.initialize_from_command_line()”

There is no interaction between unboundrot and nstruct – the problem is that unboundrot requires an argument; nstruct happens to be the next thing so that’s when you see an error. You should be seeing an error even without the last line present (but I’m perfectly willing to believe you do not).

As far as I can tell, the file format for the unboundrot flag is PDB-formatted residue records; I don’t think they have to be sorted in any particular way. I think you can just put whatever coordinates you want in, but the obvious thing is to copy-paste them from the PDB you want it to refer to. It appears to do internal matching by reading the PDB number/chain and matching to the Rosetta numbering for the residue. There is an example in your copy at rosetta_source/test/scientific/cluster/multi_residue_ligand_docking/; the python script shows that the /unbound_from_kwk folder is used as input to unboundrot.