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Structure prediction

Segmentation fault when running Abinito Relax

Category: 
Structure prediction

Hi everyone,
I try to using AbinitioRelax of Rosetta3.4 to predict the structure of a amino acid sequence (308 residues).
However, even when I used the simple flags file (with no option for optimal performace) that just required the fasta and fragments input files, the script couldn't be run.
Error was "Segmentation fault 11"
First I thought my input file had something wrong, then, I tried to run the demo script (rosetta3.4/rosetta_demos/abinitio) with full inputs file and the flags file like below:

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How the Rosetta score (dG) is actually related to dH (enthalpy) and dS (entropy)?

Category: 
Structure prediction

Dear Friends,
As we know, dG=dH-TdS. In Rosetta total score, the dG is broken down into a range of contributions with different weights. Can we assign some of those contributions to dH and some to dS? How does the temperature T play the role in Rosetta total score? Thank you very much.

Yours sincerely
Cheng

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What is the total_score that relax outputs?

Category: 
Structure prediction

I ran relax on a structure downloaded from pdb (after I cleaned it using PyRosetta's cleanATOM()), following the instructions here: https://www.rosettacommons.org/docs/latest/preparing-structures.html. The exact command I used is this:

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Suggestions for email notification & "category" for post

Category: 
Structure prediction

Dear Rosetta developers,
Can I suggest some improvement?

1. The register users can subscribe to receive email notification about the Rosetta events. It is very good that recently we can receive notice when our post is replied. This may be extended to other events as well. For example, now the "User Guide" is not available at the moment. It would be great if we can get email when it comes back to work again.

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Why there are two outputs using pmut_scan_parallel.linuxgccrelease with a mutant list file?

Category: 
Structure prediction

Dear friends,
I am using pmut_scan_parallel.linuxgccrelease to mutate a residue with a mutant list file. There are two PDB outputs for the point mutant. The two outputs are of slight difference at the mutated region. Can I ask why there are two outputs, and which one should I choose?

The original PDB and two outputs are attached.

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ignore loops on threading

Category: 
Structure prediction

Hi there,
Is there any way to ignore some loops on threading? I'm trying to build a model based in a template which is about 30% identical to the query sequence. The sequence has lots of loops ranging from few aa to 80 aa. I was wondering if would be possible to ignore the biggest loop(s) at first and loopmodel them in a separate protocol.
Looks like the some loops are not closing so as the program finishes without build any model.
Perhaps someone could suggest a better approach.
Best,
Fred

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