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Docking

zero standard deviation of I_sc in protein-protein docking

Category: 
Docking

Hello,

I ran protein-protein Rosetta docking for 50 output structures. The I_sc of the output structures (50 structures) are so close to each other in such a way that their standard deviation is so close to zero(around 0.03). I was wondering what this means. Does it make sense MC sampling of Rosetta gives me identical results?

 

Thank you

Post Situation: 

ligand_docking: ligand preparation

Category: 
Docking

Hi, I am using mol-to-param script to generate param files of my conformer. the sdf file looks normal before generation. But the PDB looks weird with some bonds connected to each other when I visualize it in pymol software however it looks totally fine in chemdoodle3D. Anyone has any clue about this? 

The PDB with weird structure looks like this:

Post Situation: 

How to create a native file for Protein-Protein docking

Category: 
Docking

Hi,

 

We are trying to dock two proteins, let say protein A and protein B. From tutorials (https://www.rosettacommons.org/demos/latest/tutorials/Protein-Protein-Docking/Protein-Protein-Docking), they say we need native but we having a hard time to understand how to create the native file. If someone can help us it would be great.

 

 

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How to select docked models

Category: 
Docking

Dear all, 

I have generated 500 docked complex model with docking_protocol.linuxgccrelease using a command like this:

docking_protocol.linuxgccrelease\
  -s start_prepacked.pdb\
  -partners A_B\
  -dock_pert 3 8\
  -ensemble1 prot1_ensemble.list\
  -ensemble2 prot2_ensemble.list\
  -out:path:all docking\
  -nstruct 500 | tee docking.log

Post Situation: 

How to create a native file for Protein-Protein docking

Category: 
Docking

Hi,

 

We are trying to dock two proteins, let say protein A and protein B. From tutorials (https://www.rosettacommons.org/demos/latest/tutorials/Protein-Protein-Docking/Protein-Protein-Docking), they say we need native but we having a hard time to understand how to create the native file. If someone can help us it would be great.

Post Situation: 

error when using script best_ifaceE.py

Category: 
Docking

Hi I have output my ligand-docked pdbs in silent out as both pdbs and in binary but regardless when I run the script to identify the top 10 percent based on IF delta score I get the following error.

 

FILE]: src/protocols/jd2/AtomTreeDiffJobInputter.cc

[LINE]: 132

[START_MESSAGE]

[ ERROR ] UtilityExitException

ERROR: No valid input structures found for AtomTreeDiff file.

 

 

 

[END_MESSAGE]

[END_CRASH_REPORT]

 

Post Situation: 

Constraint generator

Category: 
Docking

 

Question on using HydrogenBondConstraintGenerator

 

The score function I am using is ref2015.wts. It is said that to apply constraint properly, the scorefunction being used needs to have a non-zero weight for the appropriate constraint score term. Does that mean I need to add coorndinate_constraint, atom_pair_constraint or/and angel_constraint into ref2015?

 

If I want to apply for constraint while docking, but want the original score (without constraint) to be displayed. Do I set mover like this?

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