flexpepdock flag “-packing:unboundrot”

[Anonymous]

I’m running flexpepdock with the flag “-unboundrot” and getting this error when I set the -nstruct flag manually (versus using the default of 1).

>[path to rosetta]/FlexPepDocking.linuxgccrelease
-database [path to db]
-s input.pdb
-native native.pdb
-receptor_chain ‘A’
-peptide_chain ‘H’
-rbMCM
-torsionsMCM
-rep_ramp_cycles 2
-ex1
-ex2aro
-mute core.io.database
-mute core.util.prof
-mute protocols.jd2.JobDistributor
-unboundrot
-nstruct 1

ERROR: No values of the appropriate type specified for multi-valued option -packing:unboundrot

In general, where can I find how to use flags? There is no entry about this flag on the flexpepdock page in the Rosetta User’s Manual.

[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.

[Anonymous]

Provide a pdb file!
You forgot to provide a pdb file from which the additional rotamers will be taken (i.e. the unbound rotamers). If you add that file, you should be set. Note also that there is a detailed description in the manual on page http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/app_flexpep_docking.html. Just look for “-unboundrot”.

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