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Problems with ICOOR when generating polymer params file

Category: 
Non-Canonical Peptides

Hello,

We're trying to incorporate a nonanonical amino acid (3, 5-Difluorotyrosine) in my enzyme design protocol. We've been using the molfile_to_params_polymer.py script provided in the demos folder; however, the params file isn't generating correctly (the file is attached below as DFT.params). When running enzyme design protocol, we get the following error:

             "Only the third ICOOR atom in a topology file should list itself as its own dihedral atom"

Post Situation: 

ERROR: Unable to open weights/patch file

Category: 
Scoring

Hello,

I am getting the following error:

ERROR: Unable to open weights/patch file. None of (./)ref2015 or (./)ref2015.wts or /cluster/rosetta/bin/mpi/../database/scoring/weights/ref2015 or /cluster/rosetta/bin/mpi/../database/scoring/weights/ref2015.wts exist

Post Situation: 

ERROR: Your compiler does not have full support for C++11 regex, and therefore can't support RegEx_based_CDR_Detector/antibody g

Category: 
Structure prediction

Hi there,

I tried to do antibody modeling, however, there is complie issue shown as the following:

$ROSETTA/bin/antibody.linuxgccrelease -fasta 27666.fasta | tee grafting.log

Post Situation: 

Temperature

Category: 
Structure prediction

Hi,

I was wondering if it is posible to measure the free energy or stability of one protein in diferent temperature environments. Would this be done by changing the temperature of the energy minimization? And if so, how do I do it? I haven't found a specific flag for this purpose.

Thanks.

Post Situation: 

Urgent issue: Error with submitting a new Rosetta-Vienna RNP-ddG job

Category: 
ROSIE

"Submitting Rosetta-Vienna RNP-ddG job failed!

Validation failed as:

  • seq_file: Incorrect seq_file format. Each line should have the format:
    sequence RNAfold_energy

    For example:
    gggggggaucaccccccc -4.5

 

Please correct this errors and re-submit!"

Post Situation: 

Unknown Element "SE" when generating NCAA params file containing selenium

Category: 
Non-Canonical Peptides

Hello,

I've been trying to incorporate a noncanonical selenium-containing residue into my protein sequence, however, when running molefile_to_params_polymer.py I keep getting an error saying "unknown element SE." I've tried looking at the code where the error occurs, and it seems there are a series of elif statements that specify some atoms that are allowed. That being said, I swapped selenium out for xenon (not listed in the code) in the sdf file and the function ran to completion. I've attached a screenshot of my SDF.

Post Situation: 

Include MHC alpha helices in loop modelling protocol for pMHC complex

Category: 
Structure prediction

Hi,

I am using rosetta for modelling the peptide from a pMHC complex. I have been using a template which I thread into the target sequence which I use in a loop modelling protocol. 

When modelling I only focus on the peptide without letting any part of the MHC move, but in some cases, I have bad modelling results.
I was wondering if including the residues of the MHC in contact with peptides in the modelling will be a way to improve the results I am getting.

Post Situation: 

pMHC modelling

Category: 
Structure prediction

Hi,

I am using rosetta for modelling the peptide from a pMHC complex. I have been using a template which I thread into the target sequence which I use in a loop modelling protocol. 

Until now the templates that I used had a high sequence identity with the target, but now I have cases where the identity is 3 out 9 or even less.

My question regarding this is:

Post Situation: 

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