Off topic: PyRosetta unrecognized aa Ur

From: Eike Schulz
Date: 8 February 2012 16:29

Hello everybody,

This is slightly off-topic but I still hope there might be somebody in the crowd with (Py)Rosetta experience. I successfully tried protein_protein docking before, but now I am trying to dock a RNA into a protein using PyRosetta v.1.1, which, as you can imagine, fails in a new an unusual way ;) …  

I used the dna_dock.py script provided. When I run the script it finishes with following error message: 

ERROR:  unrecognized aa  Ur

ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 629

Traceback (most recent call last):

  File "rna_dock.py", line 6, in <module>

    pose_from_pdb(p, "rnadock.pdb")

RuntimeError: unidentifiable C++ exception

Obviously PyRosetta doesn't recognize the RNA specific residues – and is still in "DNA-mode". Looking fot hints in the internet took me to this website (http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/RNA_protein_changes.html), I followed the instructions changing files and pathes but still I receive the same error message. 

Below I posted the respective changes that I made according to the recommendations in ˜/PyRosetta/rosetta_database/chemical/residue_type_sets/fa_standard:  

My residue_types.txt

## Nucleic Acid Types

#residue_types/nucleic/ADE.params

#residue_types/nucleic/THY.params

#residue_types/nucleic/CYT.params

#residue_types/nucleic/GUA.params

residue_types/nucleic/RAD.params

residue_types/nucleic/RCY.params

residue_types/nucleic/RGU.params

residue_types/nucleic/URA.params

#residue_types/nucleic/GNP.params

#residue_types/nucleic/GDP.params

#residue_types/nucleic/GTP.params

My patches.txt: 

patches/CtermProteinFull.txt

patches/Cterm_amidation.txt

patches/NtermProteinFull.txt

#patches/LowerDNA.txt

#patches/UpperDNA.txt

patches/LowerRNA.txt

patches/UpperRNA.txt

patches/SpecialRotamer.txt

patches/protein_cutpoint_upper.txt

patches/protein_cutpoint_lower.txt

patches/VirtualBB.txt

patches/ShoveBB.txt

patches/VirtualDNAPhosphate.txt

patches/VirtualNterm.txt

patches/RepulsiveOnly_fa.txt

patches/VirtualProteinResidue.txt

Do you have any ideas what could have gone wrong – or what else I need to do in order to make it work? 

Many thanks in advance and best regards

Eike