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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
Hi Rosetta community,
Hoping someone can help me with this issue I'm having! I'm trying to dock a cofactor and a ligand into an alphafold model using Rosetta match. Essentially, I know which residue is supposed to be covalently bound to the cofactor, so I've made that the first constraint block of the CST file. Then, I am trying to match the ligand with the cofactor. This is constraint block #2 and as such I have included the following lines at the end of CST block 2 (since I'm matching essentially ligand 1 to ligand 2).
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?
I'm new to Rosetta, and I'm currently attempting to create a params file for docking water as a secondary ligand in my docking experiment. I'm using the following Rosetta script for this purpose:
Rosetta/main/source/scripts/python/public/molfile_to_params.py -n X00 -pX00 --conformers-in-one-file 0001H2O.mol2 --keep-names --chain D
However, I'm encountering an error message that reads: "ValueError: No acceptable neighbor atoms in molecule!"
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