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_p
rotein_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
