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Structure prediction

Combine flags file with command line arguments?

Category: 
Compilation
Structure prediction
Docking
Design
Scoring
Enzyme Design
Loop Modeling
Constraints
Symmetry
Small Molecules
Chemically Modified Residues
Fragment Generation
Membrane
Non-Canonical Peptides
Nucleic Acids
Phenix / MR Rosetta

Is it possible to combine a flags file with command line arguments?

For example, something like this:

minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file

where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:

minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list

Thanks.

Post Situation: 

Segmentation fault

Category: 
Structure prediction

Hi everyone,
I tried to run protocol AbinitioRelax to predict the structure of a sequence amino acid.
Howerver, I just could run this protocol with less than 11 cores (CPU processor). If I increased the core number more than 11, the protocol couldn't be run, even my PC has 12 or 16 processor. It returned the "Segmentation fault (11)" and cancel the job.
It doesn't happen the same problem when I run the protocol Flexpepdock.
Did anybody meeting the same problem with me?
Can anybody help me solve this problem?
Thank you so much.

Post Situation: 

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:

Post Situation: 

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

Post Situation: 

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:

Post Situation: 

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.

Post Situation: 

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.

Post Situation: 

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