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Loop Modeling

Segmentation Fault

Category: 
Loop Modeling

Hello! I'm trying to run add some missing loop to my protein by appear segmentation fault as error.

Anyone have an idea to solve this issue?

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Post Situation: 

I want to refine my pdb file,but it has multiple breaks or has multiple loops missing resi

Category: 
Loop Modeling

Take 6A5E for example,it has multiple breaks. i try to feed a blueprint file with all loops,however it turn out only the first loop was remodel .guess what when i view it in pymol i still got the same number of break .

here is my command$> mpiexec -np 18 remodel.cxx11threadmpiserialization.linuxgccrelease @missing_resi_loop

and my flag file 

-loops
-in:file:s FER-LLG2.pdb
-remodel:blueprint ferllgb.remodel

-run:chain B
-remodel:num_trajectory 1
-remodel:quick_and_dirty

Post Situation: 

error in loop remodeling

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

Post Situation: 

Protein Protein Docking with Linker

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

Post Situation: 

Segmentation fault with nstruct > 1

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?

 

 

Post Situation: 

Loop modeling

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

Post Situation: 

GeneralizedKIC disulfide closure

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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Antigen-antibody modeling

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."

Post Situation: 

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