You are here

Home

Docking

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

Submitted by alove1 on Sat, 2023-10-28 17:19
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).

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

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

Submitted by lei on Mon, 2023-09-11 23:34
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!

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Generating Params File for water molecule

Submitted by Ahmed Raslan on Thu, 2023-08-17 13:13
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!"

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

RosettaDock - protonation states

Submitted by LWilliamson on Tue, 2023-08-15 08:15
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

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

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

Submitted by Jane_002 on Tue, 2023-08-08 21:07
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:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

GALigandDock errors

Submitted by Delfosse57 on Mon, 2023-08-07 13:16
Category: 
Docking

Hello,

I am attempting to use the GALigandDock mover to perform dockings of a metal ligand similar to heme. I am following this paper: https://pubs.acs.org/doi/suppl/10.1021/jacs.3c02742/suppl_file/ja3c02742_si_001.pdf.

I generated a params file using the molfile_to_params script, and proceeded to use the exact same command and docking xml file.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Questions about gen_apo_grids

Submitted by JasonIsaac on Sat, 2023-06-17 00:20
Category: 
Docking

Hi, everyone:

    I want to generate pos file for different scaffolds, and I find that gen_apo_grid can satisfy my needs. But there is a problem, if this option "-packstat:surface_accessibility"  is on, I can set the value of "-packstat:min_surface_accessibility". Whatever value I set for "-packstat:min_surface_accessibility", the output pos file does not change at all. 

Example Command Lines: 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Pages

Subscribe to RSS - Docking