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Structure prediction

rosetta_cm segfault

Category: 
Structure prediction

I set up a homology model with the setup_RosettaCM.py
It creates a set of threaded models, an xml file with commands, and a flags command that points to the input file and the xml. When I run the rosetta_scripts command with this flags and xml, I get a segmentation fault. I find the error messages difficult to understand. 

Here is the command, screen output, flags, xml, and CRASH.log

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How to provide multiple templates for Robetta with RosettaCM option?

Category: 
Structure prediction

The FAQ of robetta said "You can load multiple templates, modify the alignments, add constraints, and more before submitting.“ However, I cannot find the option for loading multiple templates on the Robetta webserver. Is that possible?

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RosettaCM: threading okay, but hybridize loses many secondary structure

Category: 
Structure prediction

I use two templates to run the RosettaCM, each template representing different parts of the target. The threading step can retain most of the secondary structure. However, when doing the hybridize step, one part in the target loses half of its beta-sheets. Is this a common issue?

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RosettaCM: "Ligands must be added to all templates"

Category: 
Structure prediction

The RosettaCM requires Ligands must be added to all templates with a non-zero weight in the XML file!

In my case, the templates represent different parts of the target, so some template includes the ligand while some template does not. Do I really need to add the ligand to the template that does not have the ligand?

If it is necessary, how to do it? It is not likely to use some alignment to "estimate" the ligand location in the template.

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Add a ligand with only one atom (i.e. Zn) to the RosettaCM

Category: 
Structure prediction

My understanding for adding the ligand is to use the molfile_to_params script to generate XXX.cen.params, XXX.fa.params, XXX.tors files. 

My ligand is just a one atom Zn. When molfile_to_params script is used, I got this error

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How to Perform point mutations with NCAA

Category: 
Structure prediction

Hello Everyone,

I am trying to mutate multiple residues of a peptide with NCAA to determine their structure and ΔΔG of mutation on Rosetta. 

I would be grateful if anyone could share any research article, material or guidance to proceed on this matter.

 

P.S. - I am a beginner at Rosetta without any bacl ground in coding or bioinformatics. Any help and advice is appreciated.

 

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Obtaining all PDB IDs containing similar binding sites for a specific ligand

Category: 
Structure prediction

Hi all, 

Is it possible to search the proteins having similar binding sites for a specific ligand in Rosetta? I need to classify proteins based their binding site similarities -in terms of RMSD. If it is possible, how can I do this? Thanks in advance. 

 

Antonia

 
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Internal error while running AbinitioRelax

Category: 
Structure prediction

I am trying to learn Rosetta without any background computer science or bioinformatics. I tried to run the AbinitioRelax.default.linuxrelease program with the proper input files and got the following internal error -

[FILE]: src/core/chemical/GlobalResidueTypeSet.cc
[LINE]: 149
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Unable to open file: /home/rosetta/main/database/chemical/residue_type_sets/fa_standard/residue_types.txt


[END_MESSAGE]
[END_CRASH_REPORT]
 

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