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Nucleic Acids

Re: Protein-RNA interface design

Submitted by bharat_46010 on Tue, 2015-04-07 04:44
Category: 
Design
Nucleic Acids

Hi,

I am trying to run the protein-RNA interface design protocol present in rosetta_demos. I found that in the xml file the residues that are allowed for design are not present in the protein (1a9n_ABQ). Am I missing something here ??

I also want to know whether rosetta can score protein-RNA interactions well or not, and what extra terms are scored in calculating the binding energy of the designed interface in case of protein-RNA interactions?

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Rosetta 3 - General

Combine flags file with command line arguments?

Submitted by cossio on Mon, 2014-12-22 13:52
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.

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Rosetta 3 - General

Steric clashes in RNA minimization

Submitted by brianmlee on Tue, 2014-11-18 18:29
Category: 
Nucleic Acids

I have run into an intermittent problem with RNA_minimizer within the rna_denovo application. I am using identical setups in different directories and shells. I have two calculations currently running without problems. When I try the same calculation in a 3rd directory, I am getting high scores for lk_nonpolar and the resulting pdb structures have steric clashes with overlap side chain atoms. There are no errors reported during the calculation, but the results are not usable.

The calculation is a simple rna hairpin using rna_helix to generate the stem.pdb file:

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Rosetta 3 - Applications

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