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Structure prediction

farfar2 error

Category: 
Structure prediction

Hello

I am trying to model a 514-nt long RNA structure using farfar2. My job failed with the following error

ERROR: Not complementary at positions A    8 and U   13

I do not understand this, A and U are complementary  and I have checked both the input sequence and dot bracket files and I dont see any discrepancies. Attaching both inputs and the Rosie crash log file. Could someone please help me sort the error.

Thank you

Post Situation: 

antibody - sequence position requested was 0

Category: 
Structure prediction

Hi,

I am trying to do some antibody structure prediction. During the grafting step for the sequence I am working with, it seems to get through making 4 models, but then crashes with the error message: 

[FILE]: src/core/conformation/Conformation.hh

[LINE]: 509

[START_MESSAGE]

[ ERROR ] UtilityExitException

ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0.  Pose numbering starts at 1.

Anyone have any idea what is going wrong here? 

Post Situation: 

calcium metal nomenclature: Rosetta_cm confusing HETATM CA (calcium) with ATOM CA (alpha-carbon)

Category: 
Structure prediction
Constraints
Symmetry
Membrane

Dear community,

I had this posted under a different sub-forum but I realized it didn't fit that forum so deleted it and reposting here.

Post Situation: 

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

Post Situation: 

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?

Post Situation: 

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?

Post Situation: 

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.

Post Situation: 

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