I don't mean to beat the same drum over an over again, but the issue with designing a non-monomeric protein with a flexible backbone is important. There are two parts to my question.
Firstly, is the mvbb option in rosetta even able to handle a pdb with two chains? Even if I somehow force rosetta to run, will the results be dependable?
Secondly, is it possible to get a fragment file that contains 2 separate chains? Submitting two chains to the fragment server produces fragment files for 1 chain that has the combined sequences of the two original chains. If that is not possible, is there any way to get rosetta to accept 4 fragment files rather than two (by modifying the paths.txt file for example) so that it will design two separate chains at the same time?
I actually used the following command to run a design on a dimer with 600 total residues:
rosetta.osx aa ABCD _ -s ABCD_ideal.pdb -design -mvbb -multi_chain -resfile ABCD.rrf
The result was a pdb file where the two separate chains had a peptide bond between them (I assume this occurred due to the problem with the fragment files I mentioned above). Assuming the other problems are solved, is the command I used correct or is, for example, '-read_all_chains' better than '-multi_chain' in this situation.
Thanks a lot for the help.