We have a question regarding the starting sequence during the sequence design process when you have an initial backbone structure but no initial sequence.
We have tried submitting a random sequence to the Robetta fragment server but this results in an error due the server being unable to find any fragments.
Now given that we already have a backbone structure and would only like Rosetta to make small adjustments to the backbone - can we safely just submit any existing protein sequence to Robetta to get fragments, edit the input PDB starting structure to have a random sequence, and assume that the fragments will be ignored in the design process?
Alternatively is there a better way to ensure we start sequence design from a random starting sequence?
thank you very much for you help in advance,