Hi Rosetta team,
I am trying to generate some tertiary structures for a relatively large RNA (300+ nt) with rna_denovo. But I keep getting a strange error saying the nucleotides are not complementary:
[ ERROR ]: Caught exception:
[ ERROR ] UtilityExitException
ERROR: Not complementary at positions C 48 and G 53
I attached my secondary structure, fasta and ct file for the RNA. I wonder what's the cause of this problem. Thanks much.
Your fasta is in all capital letters, so it is interpreted as a protein sequence for consistency with the rest of Rosetta and to enable RNA modeling. It looks like you don't want to use any local templates or any "fancy" features of FARFAR2, so maybe it is sufficient for you to supply the lowercase version of this sequence directly to the -sequence flag.
Thanks for the reply.