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Loop Modeling

error in loop remodeling

Submitted by syntekabio2019 on Wed, 2023-04-05 01:00
Category: 
Loop Modeling

 

Hi I'm trying to fill the missing loop with remodel.linuxgccrelease in rosetta

for some pdb, there's no problem in filling missing loop

but I got following error with certain PDB

core.fragment.picking_old.vall.vall_io: Added 62471 sections to library totaling 1400124 residues.
core.fragment.picking_old.vall.eval.IdentityEval: ss = LLLLLLL  |  aa = .......
core.fragment.picking_old.vall.eval.ABEGOEval: abego = LLLLLLL
core.sequence.ABEGOManager: [ ERROR ] Unrecognized abego index: L

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Rosetta 3 - Applications

Protein Protein Docking with Linker

Submitted by mrinal on Mon, 2023-03-20 15:58
Category: 
Loop Modeling

Hi

I am trying to dock to two proteins where the ends should be connected by a polyglycine linker. Is there a tutorial on protein protein docking constrained by a polyglycine linker. I would want to vary the linker and see the effect on the protein protein docking.

Mrinal

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Rosetta 3 - Applications

Segmentation fault with nstruct > 1

Submitted by Brian Wiley on Sun, 2023-02-12 20:46
Category: 
Loop Modeling

I am running loop model with the remodel protocol (remodel.static.linuxgccrelease).  It succesfully can model despite ligands in the file using -ignore_unrecognized_res when a single structure is required with -nstruct 1 however as soo as I try to increase it to -nstruct 2 I get a segmentation fault.  Anyone experience this before?

 

 

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Rosetta 3 - General

Loop modeling

Submitted by Robertofg on Tue, 2022-11-22 00:34
Category: 
Loop Modeling

Hello, 

I have a basic question about loop modelling. Can I use the edges as cutpoint or they should be excluded?

For instance, if my loop goes from residues 100 to 109, can residue 100 to be a cutpoint?

Thank you in advance,

Roberto

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Rosetta 3 - General

GeneralizedKIC disulfide closure

Submitted by Ken on Tue, 2022-08-16 13:32
Category: 
Loop Modeling

Hi all,

I have been banging my head against the wall on this for a while now, and I think it's time to get help.  Here is my problem.  I'm trying to understand how to close loops in a toy example via different residues (head to tail, side-chain/side-chain, disulfide, etc) with GenKIC and I cannot for the life of me understand what the error message is trying to tell me. 

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Rosetta 3 - General

Antigen-antibody modeling

Submitted by aastha.pal on Mon, 2022-06-27 09:34
Category: 
Loop Modeling

I was getting an error while running the snugdock that I solved using the clean_pdb.py command. When I ran flags file using snugdock @flags file, another error came up saying "the antibody doesn't contain start or end of residue of cdr loop H1. Please check pdb is renumbered properly and passed -numbering scheme option matched the PDB.This could also mean missing density in the cdr loop. Loop modeling application can be used to fill missing residues."

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Rosetta 3 - General

genkic mover produced an unwanted HN - CA bond

Submitted by cttm4a1 on Mon, 2022-06-20 14:25
Category: 
Loop Modeling

I ran the tutorial placed in demos/tutorials/GeneralizedKIC/exercise1/ and successfully produced 10 output structures. However, the residue ALA32 that was encompassed by the genkic mover has unwanted HN - CA bond and HN_CB bond. All the 10 output structures have this problem, and I've attached three of them. I tried to FastRelax the strucutre after genkic mover, but the unwanted bonds were still kept.

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Rosetta 3 - General

Modelling at defined pH - for pmutscan - pH:mode not working

Submitted by cagfa1 on Tue, 2022-03-15 04:05
Category: 
Scoring
Loop Modeling
Chemically Modified Residues

Hi all, 

I am new to Rosetta and using various Rosetta protocols, primarily remodel and pmutscan, to assess the impact of various mutations on protein stability. I would like to model the protein and associated mutations at acidic pH as this may affect salt bridge formation and overall REU score.

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Rosetta 3 - Applications

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