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Docking

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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pepspec anchor dock

Category: 
Docking

What am I doing wrong?

Here is the call command:

/Users/andreserobian/Documents/rosetta/main/source/bin/./pepspec_anchor_dock.macosclangrelease -in:file:s her2+ile_ABC.pdb -out:pdb 1

Here is the output:

core.init: Checking for fconfig files in pwd and ./rosetta/flags 

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Make fragments

Category: 
Docking

Hi Everyone 

I am currently working with the flexpepdock protocol and I need to create fragments. Unfortunately my peptides are short <27 aa and cannot use robetta. I am doing the fragment creation locally but the procedure is somewhat complex, could someone help me what steps should I follow to modify the make_fragments.pl script 

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Translate mover chain X doesnot exist.

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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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

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