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Docking

Some problems with the "advanced protein-protein docking" tutorial

Category: 
Docking

I am studying the Rosetta "advanced protein-protein docking" tutorial (https://www.rosettacommons.org/demos/latest/tutorials/advanced_protein-protein_docking/advanced_protein-protein_docking_tutorial), but I find some confusing problems with it. 

Problem 1

The input file pdb file for the docking  command: 

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Problems with "pdb_renumber.py" in tutorial Advanced Protein-Protein Docking

Category: 
Docking

Dear all,

I am learning the advanced "protein-protein docking" part of the Rosetta about the docking of HA and antibody. When I input the following command in this tutorial: 

$ROSETTA_TOOLS/protein_tools/scripts/pdb_renumber.py --norestart input_files/3GBM_AB.pdb input_files/3gbm_HA.pdb

I get the following error message:

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Adding water interactions when docking a ligand with Rosetta 3.7.

Category: 
Docking

I am using RosettaScripts to dock a ligand, and I would like to include several - known - key water interactions. 

I found a demo somewhere (RosettaCon?) that showed this is possible, but I it looked like the xml was designed for a version well before Rosetta 3.7. From reading the Scripts docs, it looks like including the term minimize_water=true to the <MOVEMAP_BUILDER /> element should handle the water interactions. 

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Ligand Docking with RosettaScripts gives a ParsedProtocol exception

Category: 
Docking

I am trying to run a ligand docking simulation, and am running into a few technical limitations. I am trying to follow the tutorial form the Meiler lab (only with a different starting pdb and ligand).

I am running the command:

rosetta_scripts.linuxgccrelease -database $ROSETTA_DATABASE -in:file:s /inputs/4XXX_model.pdb /inputs/MyLigand.pdb -in:file:extra_res_fa /inputs/MyLigand.params -nstruct 3 -parser:protocol /scripts/xml/dock.xml -mistakes:restore_pre_talaris_2013_behavior true

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can not find a residue type that matches the residue HIS_P:NtermProteinFull

Category: 
Docking

Hi,

I have been trying to dock a protein and peptide at pH 5.5 using pH_mode as described by Kilambi and Gray's protocol. However, if I omit the keep_input_protonation_state flag the SFR builder removes the protons from the protonated residues. If I keep the keep_input_protonation_state flag I get a "can not find a residue type that matches the residue HIS_P" error. Is there a fix for that?

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Docking Prepack protocol working or not ?

Category: 
Docking
Scoring

Hi Rosetta community, 

I'm running the prepack protocol using as input a PDB file containing a dimer (chain A and B). The protocol seemed to work ("... reported success in 3 seconds") but I get the following warning : 

[ WARNING ] When switching to a fa_standard ResidueTypeSet:  Pose already contains fa_standard ResidueTypes.

and my score_sc file contains 0.000 for the total score for every generated structure.

Here the command I used to run prepack:

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Extremely low interface scores with "local refinement"

Category: 
Docking

Hi,

I am using Rosetta local refinement to calculate the interface scores of known protein complexes (in a bound form).

In the docking protocol, it says "Typical values for I_sc of godd decoys are in the range of -5 to -10.". However, for some complexes, rosetta local refinement gives me I_sc as low as -5988.1. This number doesn't seem realistic to me. Could you please explain why we see such small numbers? How can we interpret this result, if the good binding score is in the range of -5 and -10?

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