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Structure prediction

Temperature

Submitted by mrosam on Mon, 2022-08-08 01:37
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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Rosetta 3 - General

Include MHC alpha helices in loop modelling protocol for pMHC complex

Submitted by Roberto on Thu, 2022-08-04 07:22
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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Rosetta 3 - Applications

pMHC modelling

Submitted by Roberto on Thu, 2022-08-04 07:11
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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Rosetta 3 - Applications

Porblem with Rosetta Homology Modelling

Submitted by Karthik on Wed, 2022-07-13 23:45
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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Rosetta 3 - General

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

Submitted by yliang20 on Wed, 2022-06-15 22:22
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:

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Rosetta 3 - Applications

Could not open file /Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/citations/rosetta_citations

Submitted by yliang20 on Wed, 2022-06-15 11:26
Category: 
Structure prediction

Hi,

I installed rosetta_bin_linux_2021.07.61567 mode=debug and then ran Rosetta CM Hybridization. However, it gives the error messages as 'Could not open file /Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/citations/rosetta_citations'. I have deleted everthing with 'rosetta_bin_linux_2020.08.61146_bundle'. I do see this rosetta_citations file in my current 'rosetta_bin_linux_2021.07.61567_bundle/database/citation path. May I know why it looks for the citations file in my earlier old version? How to fix it?

Thanks,

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Rosetta 3 - Applications

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