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Docking-RMS value nan

Submitted by jlawrie on Wed, 2020-08-12 07:03
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

Submitted by rohi on Fri, 2020-08-07 15:41
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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Rosetta 3 - General

Error when trying docking protocol with different ligand

Submitted by scyphs on Wed, 2020-08-05 04:37
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

Submitted by NanB on Mon, 2020-08-03 11:38
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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Rosetta 3 - Applications

Calling SnugDock from PyRosetta

Submitted by shruthi.murali on Wed, 2020-07-29 15:10
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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PyRosetta - General

Zero residues error in docking

Submitted by cjy318 on Tue, 2020-07-28 19:47
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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Rosetta 3 - Applications

pepspec anchor dock

Submitted by Andre Serobian on Tue, 2020-07-28 05:51
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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Rosetta 3 - Applications

Make fragments

Submitted by jeanramos on Mon, 2020-07-13 00:56
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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Rosetta 3 - General

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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