Thanks for your answer. I am receiving sequences from somebody else who didn’t provide any kind of information, but you are probably right about it being DNA. I will talk to them about it.
Also, I found this information in the Robetta FAQs, dealing with possible issues when processing long sequences:
__** Begin ** __
The Rosetta folding program itself is a FORTRAN program that has to be careful with its memory usage. Extremely long sequences cannot be fit into memory, so any domain level models are limited to no more than __250 residues for the de novo protocol__, and __600 residues for the comparative modeling protocol__.
The de novo protocol suffers, as do all such methods, from a limitation in the ability to sample conformations available to the protein. Larger targets that are high contact-order are more difficult to sample in a reasonable amount of computer time, and probably require much larger decoy ensembles than the Robetta server can afford to generate. Therefore, we impose a de novo domain size limit of about 200 residues, which is clearly often incorrect, but necessary. It is hoped that in such cases, features of the target are still captured by the models.
There is additionally a limit on the length of the full chain of about 1000 residues, so that the independently modeled domains may be assembled into a contiguous chain.
__ ** End ** __
Found here: [http://robetta.bakerlab.org/faqs.jsp#long_sequences|http://robetta.bakerlab.org/faqs.jsp#long_sequences]
There is a possibility that they are running an older version of Rosetta under the hood, but maybe it is important to consider there seems to be, indeed, some kind of length restriction.
Again, thanks for your help.