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Issue with Rosetta LinkResidues Script

Category: 
Design

Hi All,

I am trying to design a 2 fold-symmetrical protein where I want to design a selected number of residues in each half and not mutate the remaining residues in both the halves. For e.g., what I want Rosetta to do is in "Half-A, the residues at position 32, 49, 56, 65, 66 should be mutated to certain residues, and the exact same mutated residues should appear after designing position 32, 49, 56, 65, 66 in Half-B.

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Linear peptide versus cyclic peptide binding prediction

Category: 
Design

I have used ROSIE server to analyze protein-antibody interaction and predict peptide sequences of antibody that would interact with the protein.

The analysis revealed 3 hotspots of the antibody sequence as in the picture attached. It did make sense to me that the predicted linaer peptides from antibody sequence were chosen from 1st and 3rd hotspots from the figure with highest contact points with the protein.

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Rosetta Remodel - Error in core::conformation::Conformation::residue(): The sequence position requested was 0.

Category: 
Design

Dear caretakers/kind strangers,

I ran into an error that i do not understand when trying to do de-novo modelling of a helix linker using REMODEL. When i leave the blueprint file without any new residues it runs fine. But when i add new residues at the end (C Terminal) the program recognizes it is a C terminal extension, but throws this error. 

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Symmetry mode in Remodel for N-terminal extension

Category: 
Design
Loop Modeling
Symmetry

Hello, 

I am trying to use Remodel for N-terminal extension of my homotetramer. I am passing in a single subunit (chain A) and symmetry file (4 subunits identified) with my blueprint with the extra residues of interest. I am getting the following error: 

File: src/protocols/loops/loops_main.cc:253
[ ERROR ] UtilityExitException
ERROR: Can't build a fold tree from a loop with an unspecified cut point.

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Errors in Interface design  

Category: 
Design

Hello there, Now I'm trying to optimize the protein sequence at binding interface for increased affinity to its target. A complex structure was previously solved by X-ray crystallography (PDB 3rh8). To make their affinity higher, I would like to design the protein sequence at both sides. Meiler Lab provides a step-by-step tutorial at his website (http://www.meilerlab.org/index.php/rosetta-tutorials). According to his tutorial, I tried, but I found something like error.

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running in MPI mode and multiple scores per output PDB file?

Category: 
Design
Scoring

Hi Forum 
I recently did a Rosetta fixbb run with MPI and found that the score file had a lot more lines of output than there were actual PDB files. Specifically, I've got 353 scores in score.sc but only 12 PDB files.  is it possible that the parallel processors are simply overwriting the PDBs?   Is there a flag I should be including to avoid this? 

Thanks!  

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Alanine Scanning for 1 Protein (no interface)

Category: 
Design
Scoring
Enzyme Design

Hi, does anyone know how to do alanine scanning for just one protein?

I looked at different movers for RosettaScripts, like ddgScan, AlaScan, and ddg. Can any of these be used for a single protein with no interface? I want to see which protein residues are good targets for mutation.

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cryptic error "Got some signal... It is:15" -- an issue with 'fixbb', or something else?

Category: 
Design

Hello Forum

I'm trying to run fixbb on my cluster here, and everything seems to have been going well for a while, but it suddenly stopped and spit out the following in the log file:

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Segment File Gen - no ouput

Category: 
Design

I am in need of some major help. 

I am running the SEWING application because I am copying the secondary structures that fit onto a particular primer, and some key binding residues are located on the loop between two beta strsnds - so I need to generate a new segment file with a few beta strands. 

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Error with RosettaAntibodyDesign when running antibody_designer.linuxgccrelease

Category: 
Design

Dear friends,

As a new learner of rosetta, I encountered an error "chain_id A represents more than one chain!" after I downloaded the 5ugy.pdb file from RCSB PDB database and renumbered to the AHo Scheme with PyIgClassify Server.

If anyone can help me with this issue? Any help would be appreciated.

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