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Docking

Python2 script in Rosetta3.13

Category: 
Docking
Good morning,

    I am trying to use Rosetta (v3.13) for  drug screening analysis and I 
    found a specific script in the Rosetta3.13 package (also in other 
    versions) which has some python2 code that hampers its use in the 
    current python3.

    The script is: 
    rosetta_bin_linux_2021.16.61629_bundle/main/source/scripts/python/public/batch_molfile_to_params.py

    Python2 code:

    1) Lines 110, 114, 117: print without brackets

    2) Lines 40, 116: "is not" instead of "!="
Post Situation: 

How to set start coordinates for ligand when doing protein_ligand docking

Category: 
Docking

Hi,

I am new to rosetta and I want to perform protein-lignad docking using rosetta3.13, I used my own PDB files and the option.txt, dock.xml under the folder rosetta/main/demos/tutorials/ligand_docking to perform docking. I found the ligand was still outside the protein after docking. Therefore, I tried to add the start coordinates for the ligand in the dock.xml but didn't find a right way. Could you help me with this?  I attached the PDB file I used for docking.

Thanks,

Huanhuan

Post Situation: 

How can I use InterfaceScore terms in docking as GenericMonteCarlo criterion

Category: 
Docking

Dear Sir/Madam, in my .xml script, I wish to use a if_X_scoreterm,  from InterfaceScoreCalculator mover, such as interface_delta_X as GenericMonteCarlo criterion but this term cannot recognized by Rosetta. There is no such kind of score_type. I wonder if there is way to do so?

 

Thanks

Best Regards

Rico

Post Situation: 

Extracting a part of a silent file as another silent file

Category: 
Docking

Dear all,

I generated a silent file as a result of a docking refinement with FlexPepDock. I want to anaylize the top 10% of the solutions (1000 decoys) and cluster them.

First, I extracted the top 10% by sorting the I_sc with:

sort -n -k2 example_score_file.sc | head -n 1000 | awk '{print $2 "\t" $25 "\t" $NF}' > score_I-sc_tag.dat

Post Situation: 

FlexPepDock ab initio: behavior without fragment files

Category: 
Docking

Hi there,

I've noticed that the FlexPepDock ab initio protocol will run even if fragments aren't specified. It also appears during these runs that the peptide backbone is flexible, varying between samples.

When no fragments are specified, what does the FlexPepDock application do to ab initio model peptides exactly?

Is there a 'default' set of fragments?

Thank you!

Nathan

Post Situation: 

D-amino acids tripeptide docking.

Category: 
Docking

Dear Rosetta Users, 

I'm going to run a molecular docking simulation of a tripeptide - small protein (around 150 aminoacids) complex.
The tripeptide consists of all D-amino acids and has about 20 rotatable bonds. 

Which application -- between RosettaLigand and FlexPepDock -- is better to dock such a small and high-flexible peptide ?
Moreover, I'd like to know which is the most up-to-date protocol to incorporate non-canonical amino acids into Rosetta.

Thanks in advance!
Samuele  

Post Situation: 

Error running D100_Docking.py

Category: 
Docking

Hello,

So I am trying to run the D100_Docking.py on PyRosetta4 that I have installed on Windows 10 Bash shell. I am just trying to use the script as is before attempting my own PDB files. Below is what I did, along with the errors:

 

Any help is greatly appreciated!

 

(base) jrodriguez@DESKTOP:/mnt/c/Windows/system32$ cd /mnt/c/Users/jrodriguez/Documents/PyRosetta4

Post Situation: 

Flex-pep-docking (ab-initio mode)

Category: 
Docking

Hello all,

To perform the Flex-pep-docking protocol (ab-initio mode), I need to create fragment files for the target peptide (with 8 residues). I have tried to do this with the make-fragment.pl script . However, I get the attached error. I have already installed the last version of Blast tools. please let me know what is the problem and how it can be solved?

Post Situation: 

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