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Docking

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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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:

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