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Docking

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)

 

 

Post Situation: 

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:

Post Situation: 

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.

 

Post Situation: 

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

Post Situation: 

How do you combine two .pdb protein structure files of the same protein?

Category: 
Docking

I have a *.pdb file of one protein. I need to do protein protein docking for this protein (I have the original one and I will also make a duplicate of it). What is the best way to combine the original one and the duplicated in one pdb file (I'm doing this to prepare the final pdb for docking).

Post Situation: 

how do i unding properly?

Category: 
Docking

Hello guys,

 

i am new to pyrosetta and I am having some issues with making sure I am undocking properly. 

I have a pdb file with a receptor with a receptor, 2 metal ions, a cofactor and then a substrate. It is arranged in a pdb file, with the receptor + metals beeing chain A, cofactor B, ligand X.

 

how do i unbind only the X chain properly? The tutorial is set up for a different problem, and i am struggling to valdidate the results. It also said that you could use 

Post Situation: 

Prevention of the negatively charged Nitrogen protonation by coupled_moves

Category: 
Docking
Small Molecules
Chemically Modified Residues

Dear sir and madam,

I have met with the unfavourable addition of 2 Hydrogen atoms onto sulfonamide Nitrogen instead one (NH2 instead of NH) on a ligand during the coupled_moves docking application runs. It is perfomed by the following command:

Post Situation: 

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