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Docking

Strong bias in sampling observed in RosettaDock

Submitted by chenna on Thu, 2020-08-27 22:23
Category: 
Docking

Dear Rosetta Community,

I am interested in flexible blind/global docking of a monomer to generate homo-dimers. For this I have used the RosettaDock application with -ensemble1 and -ensemble2 flags after passing the prepacked structure to -in file:s. I observe a strong bias in the output population of the docked dimers depending on what I pass in -in file:s. The docking commands are as follows:

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Rosetta 3 - Applications

what factors determine the lowest (best) LigInterfaceEnergy score?

Submitted by jmaly on Wed, 2020-08-26 13:07
Category: 
Docking
Scoring
Small Molecules

Hi everyone.

We are docking small molecule ligands into non-enzyme proteins to get an idea of ligand distribution/convergence within the binding pocket, using the LigInterfaceEnergy mover. While the results are promising, ligands with the lowest LigInterface energy are sometimes outliers within the ligand distribution. There is no native structure to compare to other than the input pose.

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Rosetta 3 - General

Global Docking with carbohydrates

Submitted by ChiauShu on Sat, 2020-08-22 20:16
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!

Submitted by Rob_Barringer on Tue, 2020-08-18 06:40
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

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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Rosetta 3 - Applications

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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Rosetta 3 - Applications

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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