Docking

I'm doing protein-protein docking, in which the C-terminus of one of my protein chains (PDB: 2ew4) was amidated, and when I submitted it to Rosetta and ran docking_protocol.static.linuxgccrelease, I found that the amide was automatically disassembled, how can I make it so that it doesn't happen?

2ew4_ 1.pdb is the structure before docking, 2ew4_ 2.pdb is the structure after docking

In https://github.com/RosettaCommons/PyRosetta.notebooks/blob/master/student-notebooks/06.08-Point-Mutation-Scan.ipynb

There is a unbind function:

Dear Rosetta users,

Is it possible that we could use Rosetta flexpepdock to dock a cyclic peptide (backbone cycle, disulfide cycle, or chemical linker cycle) with non-canonical amino acids to protein target?

It seems we could model the structures for such cyclic peptide with non-canonical amino acids using Rosetta, but I am not sure their docking methods.

If not, could you please recommend a docking program in Rosetta or other software for this application?

Thanks!

Hello, 

I'm attempting to compare protein-protein docking at pH 7 / 11. I've protonated my structures using PROPKA and have performed pre-packing and docking using the following commands:

docking_prepack_protocol.static.linuxgccrelease -database /apps/local/biology/rosetta/2020.11/bundle/rosetta_bin_linux_2020.11.61179_bundle/main/database/ -in:file:s model_5.pdb -unboundrot unbound_rotamers.pdb -nstruct 25 -partners A_B -ex1 -ex2aro