Now, we use rosetta to generate the backbones of proteins, and then use other program to generate sidechains. Is Rosetta able to generate pdb file of all-atom structure of a protein? How to do it?
Most Rosetta modes output the sidechains. I assume you’re using abinitio mode without some of the fullatom flags. The abinitio documentation might tell you how to do it. If abinitio doesn’t say, then the fixbb executeable will happily add sidechains for you.
I would suggest flags something like this:
-packing:repack_only
-ex1 -ex2 -ex3 -ex4
-extrachi_cutoff 0
-minimize_sidechains
-run:min_type dfpmin_armijo
.
