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Docking

Docking high and low resolution

Category: 
Docking

Hello,

 

I need to know about the method that is used for both high and low resolution docking. I know it is markov chain monte carlo, but I need to know in more details. Could you please provide me with a paper or any other resources about the method used for docking (in details)?

 

Thank you very much

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Protonating all possible sites: the problem in MOL2 file format or the innate Rosetta feature(bug)?

Category: 
Docking
Small Molecules
Chemically Modified Residues

Dear Sir and Madam,

I have performed a lot of attempts in order to conduct the coupled_moves docking with ligand without it protonation. I need to specify that this ligand (in his physiologically active form) has only one Hydrogen on his sulfonamide site. Nevertheless, despite the absence of any other Hydrogens both in input .params, MOL2 and PDB file, a lot of sites (sulfonamide Nitrogen with additional undesirable Hydrogen, as well as some Carbons on a benzene ring and tail) get protonated.
By the way, Ligand_Dock application also protonates all possible ligand sites.

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Assesing the docking

Category: 
Docking

Hello,

I followed the tutorial, and did docking. Now, I can see that the complex structure that I predicted is completely match the true complex structure. But, when I use TMalign and TMscore, they give me something like the following:

Name of Chain_1: predicted.pdb
Name of Chain_2: true.pdb
Length of Chain_1:  289 residues
Length of Chain_2:  579 residues

 

TM-score= 1.00000 (if normalized by length of Chain_1)
TM-score= 0.49914 (if normalized by length of Chain_2)

 

 

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Undesirable behaviour of PoseFromSFRBuilder regarding Hydrogen atoms

Category: 
Docking
Small Molecules
Chemically Modified Residues

Dear Rosetta people,

I am trying to dock ligand, which possesses by sulfonamide NH group to the target protein with a help of coupled_moves application by the following command:

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Constraints residues in different chain in protein-protein docking

Category: 
Docking

Hello,

 

I want to dock two proteins. I have some constraints between residues of different chain (here chain A and B).

For eaxmple:

For residues number 15 of chain A, and residue number 271 of chain B, I have the following information:

The minimum distance between residues is 0, and the maximum distance is 6.

 

How can I add constrain for something like this case (I mean when residues are in different chain)? How can I specify that residues are in diffrent chain?

 

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polymer docking using rosetta scripts

Category: 
Docking

 

   Hi  My name is  Jong hui Hong

   I'm trying to dock the ligand which has 5 chemical linked via covalent bond( ACE-UB4-DPP-GLY-GVE) using Rosetta-Scripts

   I changed ligand residue name into PRD and made conformer using obabel , made paramter file using molfile_to_params.py without any problem

   but when I run docking using  rosetta_scripts.linuxgccrelease

  I got the following error

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Extending Pyrosetta toturials for docking by adding constraints

Category: 
Docking

Hello,

I followed pyrosetta tutorials for docking.  I did something like the following:

scorefxn_low = create_score_function("interchain_cen")
jd = PyJobDistributor("output", 100, scorefxn_low)
while not jd.job_complete:
    cen_pose.assign(starting_cen_pose)
    dock_lowres.apply(cen_pose)
    jd.output_decoy(cen_pose)

 Then, I selected the candiddate with lowest score.

 

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Error: in membrane docking : Cannot split pose by membrane jump! Quitting...

Category: 
Docking

I'm trying to run the demo files of RosettaMP and it fails in the last docking step. We were able to prepack the files normally , but the last command throws error:

 

core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set.  Created 62 residue types

core.chemical.GlobalResidueTypeSet: Total time to initialize 0.016093 seconds.

protocols.docking.DockingProtocol: FOLD_TREE  EDGE 81 1 1  EDGE 1 40 -1  EDGE 1 61 2  EDGE 61 80 -1  EDGE 61 41 -1

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