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Docking

Global Docking with carbohydrates

Category: 
Docking

Hi everyone,

        I have some problems about protein and protein docking. I want to dock a peptide into protein using global docking. But there are some carbohydrates in my protein. After docking, the site of the protein bonds with carbohydrate and the carbohydrates bond each other have some error. And the score of the results are very high.

Generally, they should automatically dehydrogenate after docking. Did I miss some commands or how can I solve this problem?

I attach the output's image and following is my flag:

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Trouble running MPI docking protocol, please help!

Category: 
Docking

 Hi all,

I'm quite new to Rosetta (and computational approaches in general, I've only been using linux and bash-based interfaces for about 6 months) and I've spent a few weeks trying to understand the docking process, which I think I understand fairly well. I've run into a problem that I hope you can help me with. Apologies for any naivety/confusion/incorrect terms that I use, I'm still very much an amateur so I might not explain myself in the best way. 

What I want to do

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Docking-RMS value nan

Category: 
Docking

Hello,

I am new to Rosetta3 and jsut trying to dock some generated ligands into a protein PDB. Based on the generated structures it appears the docking program is working well however, when I look at the score.sc file the rms vlaues for all the generated structures is nan. I do not really understand if I should be expecting rms values. I am docking a ligand into an unbound protein substrate. Any information would be helpful.

Justim

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selecting pivot_residue in Backrub for ensemble generation

Category: 
Docking

Hello,

I need to generate an ensemble of proteins to capture backbone flexibility in docking. I ran relax with thorough flag, but the resultants decoys are not that much different (RMSD ranges fro 0.2 to 0.7). Then I ran Backrub without defining pivot_residue and without resfile. The resultant decoys of Backrub are also similar. Does anyone have suggestions to define pivot_residue? or how can I sample conformational space enough to consider backbone flexibility?

 

Thanks

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Error when trying docking protocol with different ligand

Category: 
Docking

Hi,

I'm coaching an iGEM team at the University of Warwick and they're doing some dock design to try to switch the specificity of a transcription factor to a different ligand. We've been able to run the docking protocol with the protein and it's native ligand and it is able to recapitualte the the native binding. However, when we try the docking protocol with the new ligand we run into this error:

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mpirun docking_protocol

Category: 
Docking

Hi all,

I was running mpi docking_protocol (docking_protocol.cxx11threadmpiserialization.linuxgccrelease) to generate 500 decoys. I got this error and only 470 decoys as output:

[ ERROR ]: Error(s) were encountered when running jobs.
12 jobs failed;
Check the output further up for additional error messages.
---------------------------------------------------------------

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Calling SnugDock from PyRosetta

Category: 
Docking
PyRosetta

I am very new to the PyRosetta platform and was hoping to get some guidance on how I can do a SnugDock run from the PyRosetta interface with an antibody pdb and antigen pdb, as I know that the ROSIE queue can be quite long. I've seen the PyRosetta 4.0 documentation for SnugDock but am a little bit overwhelmed as I'm not too well versed in Python. Any level of guidance would be greatly appreciated! 

 

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Zero residues error in docking

Category: 
Docking

Hello, I need some help.

I have no residues error during my docking process. But refining and cleaning worked well with my PDB file.

Also, 1 year ago, docking process worked well with same PDB file and older version of rosetta.

I don't know why it happened.

My PDB file is attatched. please help me.

 

It is my rosetta crash log.

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