Hi all, I have this question similar to a lot of questions in the previous posts. But I still feel a little bit confused after reading some of the replies...
Several modes of Rosetta require fragments library such as loop modeling. Currently, I working with a protein complex which contains 3 identical subunits 322 residues each). This raises several questions:
1. To simulate the whole complex, I need to ask Rosetta to read the whole complex as starting structure.
1) If there are "TER" in the pdb file, the only way to do this is add "read_all_chains" flag, right?
2) If I remove the "TER" in the pdb file, will it still work probably?
2. Since Rosetta require fragment library,
1)how do I generate this library of the whole complex? I used the Robetta server to generate my library, but when uploading the fasta file, it didn't recognize the trimer complex (322 residues each) instead of a single chain protein (966 residues).
2)So if I use the 966 residues fragment library, will Rosetta still do the modeling correctly?
Any helpful idea will be deeply appreciated!
Thanks a lot!