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Docking

SymDock with constraints

Category: 
Docking
Constraints
Symmetry

Dear all

I been trying to perform a symmetric docking with constraints and it is not working. Reading old post residue number must be carefully set. For some reason the low-res filter is dumping all the solutions ("STRUCTURE FAILED LOW-RES FILTER"). I imagine that has to be with how I define the constraints but I even tried using AtomPair CA 52 CA 182 GAUSSIANFUNC 50.0 50.0. Please can someone have a hint of what is going on?

thanks in advance

felipet

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Minimization Issue: Coarse Graining to All atom modeling

Category: 
Docking
Design
Loop Modeling

Hi all,
I want to get an all atom model of my coarse grained protein structure (after adding all the side chains back). I have been using the repacking algorithm to do so, but unfortunately its not doing the job. The side chains are not packed properly. Can you help me suggesting on how to go from coarse grained protein to get an all atom model for my protein. Is there any minimization protocol that can take care of this. Kindly let me know.

Thank you.

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Rosetta dock irmsd

Category: 
Docking

Hi Rosetta people

I have an odd problem concerning the interface rmsd output from rosetta dock.
I have two structure outputs from different runs. Only difference is using saxs as restrain in one run otherwise the scripts are identical.
I get better irmsd from the saxs run (0.333 vs. 1.116) but when looking at the structures there is barely any difference, I have checked rotamers as well.

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Output format

Category: 
Docking

Hi everyone,

I am trying to carry out some docking experiments: I have the structure of my protein in .PDB and then the cofactor NADP in .sdf.
I think that I have some problem with the output: I can only open the structure of the protein and then the .sdf of the cofactor which is not docked.

The main thing you need to know is that I am not an expert at all in this field, and I would be grateful if someone could help me to carry out the docking and visualizing it. Currently, I am using Pymol to visualize structures.

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Rosie Server Docking2, wrong plots output?

Category: 
Docking

Dear All,

Any one knows why the Rosie Server for protein docking (docking2) automatically gave two plots that seem not consistent with each other on the x-axis which is the "RMSD". Or me please give some suggestion if I understand something wrong. Please see the attached figure.

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Error while reading in silent file

Category: 
Docking

Hi all, I am facing an error, when reading in the silent output file after a docking simulation. Here I used 6 cores to create 2000 decoys each (sum 12000). See the flag file attached. I used a slightely modified version of the ligand docking application, which is provided in the ROSETTA examples.

Now, i tried to combine all six output files to compare the results. Actually, I tried it with the following command

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Relax command for docking purposes and cluster_vs_rmsd command

Category: 
Docking

Hello All,

I currently have two questions.

The first related to using the relax.linuxgccrelease,

I am relaxing a cleaned native structure to produce a 1000 decoys, in which I will cluster and use the top 5 to perform docking with Rosetta.

My question is when I relax my native structure, what options and flags should I include and not include. Should I be relaxing with contraints on the main chain and side chains, or should I relax with no constraints. Should I include -ex1 and -ex2aro flags for my purpose? Should I perform relax:fast or relax:thorough?

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Unrecognized residue Glc

Category: 
Docking

Hi everyone,

I would like to use surface_docking on a pdb containing carbohydrates.
I put as residue name "Glc" in my pdb and I added the flag:

extra_res_fa=/media/storage/a/software/rosetta_src_2015.02.57538_bundle/main/database/chemical/residue_type_sets/fa_standard/residue_types/carbohydrates/to4-beta-D-Glcp.params

However I get the following error:

ERROR: No match found for unrecognized residue at position 1
Looking for lower-terminal residue with 3-letter code: Glc
ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 1216

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Docking with Constraints in PyRosetta

Category: 
Docking

Recently I started attempting to use PyRosetta to perform protein-protein docking. I was following the PyRosetta docking tutorial at www.pyrosetta.org/tutorials and managed to get a script together that can generate a bunch of coarse models and then the best n of them are submitted to high resolution refined docking.

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