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Loop Modeling
GeneralizedKIC loop closure error
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
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
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
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
Rosetta antibody- modeling in the presense of an antigen
Hi,
is it possible to model a antibody (or just the cdr3 loop) in the presense of an antigen structure (already docked to it)?
thakns for the help!
RemodelMover and Input Pose
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De novo backbone trace from fragments
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
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.
loop modelling on complex structure
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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