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Using Rosetta Docking for nucleic acids

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Using Rosetta Docking for nucleic acids


I tried to use RosettaDock with protein-nucleic acid chains. But I have a problem. Rosetta doesn't seem to recognise nucleic acids with the parameters I used. Here is the error message:

ERROR: unrecognized aa U
ERROR:: Exit from: src/core/io/pdb/ line: 534

The version of RosettaDock I compiled (3.2.1) worked with the protein-protein complexes I tried.

I suppose there is a command to specify nucleic acids or a specific database to use. Can anybody please tell me how to use RosettaDock for protein-nucleic acid chains?

Thanks in advance.

Post Situation: 
Thu, 2011-04-28 06:16
Adrien Guilhot

U is an RNA nucleic acid. Non-RNA Rosetta executeables recognize only DNA by default, because the DNA and RNA names conflict, and the authors decided to offer one-or-the-other instead of figuring out a system for both. Are you doing RNA-protein complexes or DNA-protein complexes?

If this is not the problem it's probably a nomenclature thing. Your residue names need to match what Rosetta has in its parameter files in the database (database/chemical/residue_type_sets/fa_standard/ or something like that). Note that the RNA is NOT in the fa_standard set, but DNA is. If you're using DNA I can help you debug this path.

Thu, 2011-04-28 07:51

I've never done anything with RNA or DNA, but there's a manual page about using RNA (, although it doesn't seemed to be linked through the main documentation page. (But can be found by searching the online manual for "RNA".)

Thu, 2011-04-28 10:58

I use RNA-protein complexes. I am reading the manual page about RNA. Thank you for the link. I will tell you if I have any trouble or solution.

Mon, 2011-08-08 05:01
Adrien Guilhot