[ccp4bb] Off topic: PyRosetta unrecognized aa Ur

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: Meng-Chiao Ho mho {- at -} EINSTEIN {- dot -} YU {- dot -} EDU
Date: 2012-02-08

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Subject: Off topic: PyRosetta unrecognized aa Ur
From: Eike Schulz eike {- dot -} schulz {- at -} EMBL {- dot -} DE
Date: 2012-02-08

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 ;)
Š

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_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

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Post-doctoral position available
From: Meng-Chiao Ho mho {- at -} EINSTEIN {- dot -} YU {- dot -} EDU
Date: 2012-02-08

Next message:
Subject: Re: What happened to JAXA
From: David Schuller djs63 {- at -} CORNELL {- dot -} EDU
Date: 2012-02-08