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Docking

Error with docking_prepack_protocol while executing the tutorial "Docking Flexible Proteins"

Category: 
Docking

Hello!
I'm new at Rosetta and was doing the tutorials for protein-protein docking. I execute the command below with no problems:

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protein-protein docking

Category: 
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

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ERROR: Assertion `build_sets_[ build_set_id ].restype().has( "1HA" )` failed. ERROR:: Exit from: src/protocols/match/upstream/Pr

Category: 
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).

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Dock cyclic peptide with non-canonical amino acids to protein target using rosetta flexpepdock?

Category: 
Docking

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!

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Generating Params File for water molecule

Category: 
Docking

Greetings,

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!"

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RosettaDock - protonation states

Category: 
Docking

 

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

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[ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection!

Category: 
Docking

Hello

I'm new to Rosetta. I followed the tutorial of RosettaAntibodyDesign and ran the program well, but there was always some ' warnings ' in the log files.

 I extracted some warnings from the log file as below:

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