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using piper-flexpepdock

Submitted by syntekabio2019 on Thu, 2019-12-12 01:22
Category: 
Docking

 

 Hi

 I want to try the blind peptide docking with PIPER-Flexpepdock in Rosetta application

In Rosetta manual, it is written that 3 algorithms are there in Flexpepdock and one of them is PIPER-Flexpepdock.

But in downloaded rosetta package, I couldn't find it in main/source/bin

Where can I find it ?

or to use PIPER flexpepdock should I do something in build/install step?

Thanks

Regards

 

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Rosetta 3 - Applications

Compaing interface socre of different ligands with the same protein structure

Submitted by Caulobacter on Tue, 2019-12-10 12:53
Category: 
Scoring

I am trying to dock molecules with the same parent core but different substitution groups into the same PDB structure using ROISE. 

I tried to read through some published papers on ResettaLigand but still was not able to find out the answer for:

Since we are only allowed to include on ligand in each run, can we submit a few different runs and compare the interface score directly?

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ROSIE - General

trans-ACPC

Submitted by tttt on Wed, 2019-12-04 03:23
Category: 
PyRosetta

Hello!

I've been trying to create a pose with trans-ACPC, but when I use the X[TAC] in the sequence, it doesn't seem to know what residue it is. I know there's a params file for it... I tried loading a pdb structure with ACPC in it as my pose to see what'd happen and it says that:

"ERROR: Error in core::scoring::methods::RamaPreProEnergy::residue_pair_energy(): The RamaPrePro term is incompatible with cyclic dipeptides (as is most of the rest of Rosetta)."

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PyRosetta - Applications

Rosetta scripts crash in CM workflow

Submitted by jlburkhead on Tue, 2019-12-03 22:55
Category: 
Structure prediction

I'm trying to get started with comparative modeling for soluble proteins. I tried working through the demo/tutorial for membrane protein and adjusting for soluble, then also tried working with the RosettaCM workflow (https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/RosettaCM). I'm having no trouble creating the input files, but seem to keep getting crashes at the step of calling rosetta_scripts.

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Rosetta 3 - Applications

Docking the border segments of coiled coils in parallel orientation

Submitted by Corvin on Mon, 2019-12-02 02:00
Category: 
Docking

Dear Sir or Madam,

I need to dock the border segments of two coils (from four ones) from each of two homotetramers in a parallel orientation (I mean, that docked helix bundles should lay in one direction).

I would like to find out, which kind of files should I use and/or parameters in that files should I write for docking these segments in a proper way?

I will be sincerely grateful for your responses and advises and I am looking to it.

Best regards,

Corvin.

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Rosetta 3 - Applications

Docking Metalloprotein-Protein

Submitted by fgomes on Fri, 2019-11-22 19:12
Category: 
Docking

hi all

I try to dock one metalloprotein (ZN and Ca) to a small protein inhibitor.

I started, as suggested in the session “Working With Metalloproteins in Rosetta”, relaxing the crystal structure of the metalloprotein applying the flag -in:auto_setup_metals, in the full atom mode.

The relaxed structure and protein inhibitor were added to the same pdb file (at 20A of distance )and used as starting coordinates to the docking protocol.

 

The problem was in the Centroid Docking Phase, I guess.

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Rosetta 3 - General

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