# Structure prediction

## Error Fasta file

Category:
Structure prediction

Hello,

I am trying to predict antibody structure but I keep getting an error message when choosing the fasta file containing the heavy and light chain. I am using the ">heavy" and ">light" marker in the fasta file but it doesn't seem to recognise the sequences. I am not sure what I am doing wrong. I am attaching an image of the error message for reference.

Thanks for your help!

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## 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

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## 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.

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## 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.

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## 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:

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## CS-Rosetta cofactor

Category:
Structure prediction

Hello,

I am using Chemicel-Shift-Rosetta for protein structure determination and I would like to fix a cofactor in my protein. Does anyone have an idea how to do so?

Thanks!

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## Porblem with Rosetta Homology Modelling

Category:
Structure prediction

I am facing SEGMENTATION FAULT error when I try to generate 10000 structures in Rosetta Homology modelling. I am running this through the Batch script. For example, when I give -out:nstruct 10000 in the flag file, it generates only 48 structures after that the job gets terminated. I have attached my batch script, flag file, Error file and the Rosettta_crash.log file here. Please, can anyone help me to find the solution to this problem?

Flag File

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## ERROR: Assertion static_cast< size_type >( i - l_ ) < super::size() failed. ERROR:: Exit from: src/utility/vectorL.hh line: 42

Category:
Structure prediction

Hi,

I'm trying to generate model from CM. There is error message shown as the topic (as uploaded crash file).

'Singal 6' is given at stage 4:

Post Situation: