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Structure prediction

Unrecognized atom parameter with denovo_density

Category: 
Structure prediction

I've run into an issue building a model using denovo_density in step 4D of this protocol: https://faculty.washington.edu/dimaio/files/rosetta_density_tutorial_aug18_4.pdf,

The rosetta command that throws the error is:

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Clustering error - Help, please

Category: 
Structure prediction

Hi, I'm trying to group structures into clusters, but I have an error and an empty log file. A few months ago (in February / March) I didn't have a problem with it, although I did it in the same way (I think so). I have no idea where this problem comes from.

Using the AbinitioRelax protocol, I obtained a silent file with 100,000 structures (centroid representations) for a certain amino acid sequence. Now I want to group the structures into clusters and sort by energy. I use the following commands:

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metalloprotein ab initio with glutamic acid

Category: 
Structure prediction

Hi all,

I'm new to rosetta design and looking to do ab initio folding for my first metalloprotein design. I saw the documentation (https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/metalloprotein-abrelax), looked at the test inputs, and read the original paper. All of these only address His and Cys as ligands. Is there a way to do other ligands such as Glu or Asp?

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RosettaCM: An internal error has occurred when "Running the Hybridize mover"

Category: 
Structure prediction

Hello,

I am trying to replicate the tutorial for RosettaCM according to the following URL:

https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/RosettaCM

The step 1 (using setup_RosettaCM.py) is fine where I can obtain the thread pdb file and flags and rosetta_cm.xml.

But when I tried to run step 2 (Run the Hybridize mover). It crashed.

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"Residue 7 was disulfide bonded but had no partner" with antibody.linuxgccrelease

Category: 
Structure prediction

Dear all,

I am trying to modeling a camelid antibody with the sequence (nb.fasta) as following:

$cat nb.fasta

>heavy
QVQLQESGGGLVQAGGSLRLSCAASGTIFETEGMGWYRQAPGKEREFVATIGGGSITYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAVIAFTEHKYSYWGQGTQVTVSSLE

 

I use antibody.linuxgccrelease to model it:

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Problems with mpi version of antibody.linuxgccrelease

Category: 
Structure prediction

Dear all, 

When I run the "antibody.mpi.linuxgccrelease", like

     antibody.mpi.linuxgccrelease -fasta vhh.fasta -vhh_only | tee grafting.log

I always get the following strange information when the program approachs finishing and all grafted models have been produced:

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The usage of antibody_H3.linuxgccrelease

Category: 
Structure prediction

Dear all,

I am trying to use the antibody utinity to modeling a camelid antibody (vhh). I used the antibody.linuxgccrelease to produce 10 relaxed models for this  vhh sequence. Then I moved to do the H3 modeling. The "antibody_H3.linuxgccrelease --help" command shows many options for the antibody_H3.linuxgccrelease. However, I am a bit confused about the antibody_H3.linuxgccrelease options.

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RosettaAntibodyDesign: How can I run the protocol without allowing design?

Category: 
Structure prediction
Docking
Design

Hi there,

I am trying to use RosettaAntibodyDesigner without allowing any design elements of the protocol to occur. I understand 100% that this would remove the intended purpose and use cases of RAbD, however, I am trying to piecemeal a side-by-side comparison of a designed mAb (which works reat through this protocol) and a non-designed mAb. 

However, I would like to ensure that both my simulations are executred identially otherwise. (ie., loop flexibility in docking, etc).

Is there any way to runn RAbD while FIXing all the CDRs?

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