RNA docking

[Anonymous]

Dear all,

I successfully tried protein_protein docking in PyRosetta before, but now I am trying to dock a RNA into a protein using the PyRosetta, which unfortunately fails …

To run the docking 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
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

[Anonymous]

From the bottom of that file:

“The RNA parameter files show that the names necessary for the pdb reader to recognize RNA residues are rA, rG, rC, rU respectively so it may be necessary to edit your pdb file.”

You seem to have Ur instead of rU – that’s my guess as to what’s wrong. You’ll have to keep fiddling with the residue codes in your input….

[Author]

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