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Loop Modeling

GeneralizedKIC loop closure error

Category: 
Loop Modeling

Dear Rosetta Community,

I am trying to generate conformations for a 29 residue cyclic peptide with N-C terminal cyclisation. I've written a Rosetta Script that declares a bond between the N and C terminals and then performs a loop closure based on GeneralizedKIC.

However I am facing the following error:

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Loop modeling with constraints

Category: 
Loop Modeling
Constraints

Hi,

I am trying to model a loop with a constraints file (the constraints are for the atoms of the loop).

but every time I get this message:

[FILE]: src/core/pose/util.cc
[LINE]: 704
[START_MESSAGE]
Atom 'OVL1 31' not found

[END_MESSAGE]
[END_CRASH_REPORT]

 

I also tried to set the flag "-constraints:named" to true but it didn't help...

I am using the following command:

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MPI optimization on TACC stampede2 HPC

Category: 
Structure prediction
Loop Modeling
Symmetry
Membrane

Dear community,

I am new to MPI so please correct any misuse of terms. My question is about optimizing for MPI on an HPC or a second (preferred) solution to my issue is to optimize my RAM usage so I don't have to run MPI, serial would actually improve overall models produced anyways.

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antibody H3 modelling protocol for nanobody gives "[ ERROR ] Inaccurate G!" messages

Category: 
Loop Modeling

Hello all,

I am trying to model the H3 loop of a nanobody (VHH). The protocol runs fine and completes successfully but it gives a lot of the following error messages:

......

core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 3.8147e-06 Deriv= -0.121688 Finite Diff= 0.149698

core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 1.90735e-06 Deriv= -0.0181975 Finite Diff= 0.0799868

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De novo backbone trace from fragments

Category: 
Structure prediction
Design
Loop Modeling

Dear Rosetta experts,

I have been using rosetta mainly for refinement and iterative local rebuilding into cryo-em densities at reolustions of ~3-3.5 Angstrom. I am wondering how (or if it is possible) to combine and complete a set of backbone fragments predicted by external software into a single backbone trace using rosetta. To make matters somewhat more complicated I would need to do this without any sequence information using only polyA fragments.

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Error when using Remodel on a protein with a chemically bound ligand

Category: 
Loop Modeling

My goal is to insert a linker fragment into a protein which has a chemically bound ligand. To do that, I have relaxed the structure with the chemically bound ligand and am now trying to insert the linker fragment into my protein using Remodel. The ligand is bound to a CYX residue (modified Cystein) in my protein.

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loop modelling on complex structure

Category: 
Loop Modeling

Hi,

I'm using next-generation kIC to model one loop , which interacts with another subunit in the hetero-trimer complex.

I'd like to input the whole 3-chain structure for loop modelling as adjacent subunit could stabilize the loop conformation because of the interaction.

But I've got no idea where I can designate the chain for loop modelling if I input multi-chain structure?

Could anyone please give me some ideas?

Thanks a lot,

Tianyang

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Does antibody_numbering_converter support camelid antibody?

Category: 
Loop Modeling

Hi all,

      We downloaded Complex of a camelid single-domain vhh antibody 2P43, used Discovery Studio to change  the numbering scheme of the PDB file to  Chothia, then when we want to used "antibody_numbering_converter" to  change the numbering scheme of the PDB file from Chothia to AHo, an error occurred,  the command we used is " antibody_numbering_converter.linuxgccrelease -s 2P43_clo.pdb -camelid true -input_ab_scheme Chothia -output_ab_scheme AHo ",  the error is as follow:

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