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/file_data.cc 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.