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Translate mover chain X doesnot exist.

Submitted by surya on Thu, 2020-07-09 08:36
Category: 
Docking

Hi all,

          we are trying to run protien -ligand docking. We were able todo succesfully the tutorial and do for some of our drug molecules except "Diltiazem". we generated conformers using online tool [mentioned in the tutorial] and tried schrodinger conformers too. but the following error still persists. Screen shot is attached.

'Translate' mover" chain X doesnot exist.

We checked the conformers pdb file every conformer is seperated by 'TER' text and both PDB and conformers file has chain X.

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Rosetta 3 - Applications

zero standard deviation of I_sc in protein-protein docking

Submitted by rohi on Fri, 2020-07-03 22:19
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

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Rosetta 3 - Applications

ligand_docking: ligand preparation

Submitted by Alison_Yajie on Thu, 2020-07-02 07:05
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:

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Rosetta 3 - Applications

How to create a native file for Protein-Protein docking

Submitted by Kotimedidhi on Mon, 2020-06-22 08:10
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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Rosetta 3 - General

How to select docked models

Submitted by Sunyp_IM on Mon, 2020-06-22 00:50
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

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Rosetta 3 - Applications

How to create a native file for Protein-Protein docking

Submitted by Kotimedidhi on Fri, 2020-06-19 08:58
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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Rosetta 3 - Applications

error when using script best_ifaceE.py

Submitted by windmill on Thu, 2020-06-18 21:30
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]

 

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Rosetta 3 - General

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