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restricted fast relax changes whole structure?

Category: 
PyRosetta

Hello, 

i am trying to do a relax of a certain area of my protein, however, it seems as though the entire backbone moves (and the free energy of the entire system drops dramatically, an other indication the entire thing is beeing relaxed). My code is as follows:

working_pose = pose.clone()
sfxn = create_score_function("ref2015_cart")

Post Situation: 

Compiling rosetta to include rosetta_scripts_jd3

Category: 
Compilation

Hi,

I've currently installed rosetta3 on aws cloud vm under ubuntu OS (Ubuntu 20.04.2 LTS).

I try to use a protocol from Khersonsky et al. 2018 (PMID: 30270109).
In order to do so, a  rosetta_scripts_jd3.default.linuxgccrelease   file is needed.
However, I did not find such file under $ROSETTA/main/source/bin/ 


My rosetta version is: rosetta_src_2021.16.61629_bundle
I've compiled it with: ./scons.py -j8 mode=release bin

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: 

Topobuilder segmentation fault

Category: 
Design

I'm following the steps here https://github.com/LPDI-EPFL/topobuilder/tree/releasepy2 and got all the folders with different topologies, but once I'm in the folder and running submiter.sbatch, make_fragments protocol exits with a segmentation fault. 

Post Situation: 

duplex RNA

Category: 
Nucleic Acids

Hello,

I am using FARFAR to get the possible structures for a A-bulge RNA duplex with the following specifications:

Input sequence: CCGGCAGUGUG+CACACGUCGG

Input secstruct (((((.(((((+))))))))))

I need to keep the structure in the duplex form and not the hairpin. All output files I got with the mentioned specifications are RNA hairpins. Is there a way I can keep the structure in the duplex form.

 

thanks for yoyr help.

Best,

Amir

 

 

Post Situation: 

calcium metal nomenclature: Rosetta_cm confusing HETATM CA (calcium) with ATOM CA (alpha-carbon)

Category: 
Structure prediction
Constraints
Symmetry
Membrane

Dear community,

I had this posted under a different sub-forum but I realized it didn't fit that forum so deleted it and reposting here.

Post Situation: 

clashes created with enzdes

Category: 
Enzyme Design

 

Hello, 

I'm working on de novo enzyme design. Utilizing the enzdes application through theozyme definition. While doing regular design procedures I have noticed that Rosetta inserts amino acid identities that create clashes with the ligand. Most notable is an Ile with a distance of 3A to the ligand, instead of the minimum 4. Images attached. As far as I know, I have not altered the default behavior of vdw radii at any point.  The energies for these residues do not sky-rocket and Rosetta scores these designs very favorably.  

Post Situation: 

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