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Loop Modeling

Disulfide Bonds in Loop Modeling

Submitted by code_Monkey on Mon, 2021-05-03 08:27
Category: 
Loop Modeling

Good Morning,

I was implementing the NGK loop modeling to fill the missing loops in the PDB structure, but the disulfide bonds in the PDB were broken and converted to regular cystines after the modeling. These disulfide bonds are not in the remodeled loop region and I specified '-loops:fix_natsc true'. From the output, it says: 

core.conformation.Conformation: Found disulfide between residues 76 166

core.conformation.Conformation: current variant for 76 CYS

core.conformation.Conformation: current variant for 166 CYS

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Rosetta 3 - Applications

Filling the missing loops

Submitted by code_Monkey on Tue, 2021-04-27 07:44
Category: 
Loop Modeling

Hello,

I was working on a PDB structures with 3 missing loops. Two of them have more than 15 missing residues. In this case, are the loop modeling methods still applicable? If so, which algorithm should I follow? Can I ask if there is a better way to fill the loops without affecting the existing region in the PDB structure? Thank you!

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Rosetta 3 - Applications

GeneralizedKIC loop closure error

Submitted by chenna on Sat, 2021-04-10 00:21
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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Rosetta 3 - Applications

Loop modeling with constraints

Submitted by agctomer on Sat, 2021-03-20 03:53
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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Rosetta 3 - Applications

MPI optimization on TACC stampede2 HPC

Submitted by rlwoltz on Tue, 2021-03-16 18:07
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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Rosetta 3 - General

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

Submitted by AlfredoKCL on Sun, 2021-02-28 16:42
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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