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Design

Calculate_protein_protein_ddg

Category: 
Design

Dear Rosetta Users
I am trying to utilize the calculate_protein_protein_ddg protocol using the mutation_script.xml protocol on rosetta_2014wk52 build.
However, I am having a problem with mutating chemically modified residue (sulfated tyrosine) into a desired amino acid. I can mutate any non modified canonical amino acid to whichever amino acid I want but not the chemically modified one.

sample tail of output pdb
REMARK DesignRes. # modified amino acid mutation attempt
REMARK DesignRes, 108 H # non modified amino acid mutation attempt

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Relax with a ligand is messing up the coordinates of the ligand

Category: 
Design

Hi there,

 

I am trying to relax my structure which contains a bound ligand.

 

First, I created a LG.params file using:

python /path/to/molfile_to_params.py /path/to/1XKK_ligand.mol2

 

This file (1xKK_ligand.mol2) only contains the coordinates for the ligand from the PDB 1XKK.  molfile_to_params.py outputs the LG.params file as well as a PDB, which looks correct when visualy inspected. This is all expected.

 

Post Situation: 

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: 

algebric library for rosetta

Category: 
Design

Hi,

I'm currently integrating an application ( i developed ) with rosetta, and this app needs to perform matrix diagonalization.
The current (stand alone) application uses an open source algebric library named Eigen.
I guess that due to leagal reasons this library cannot be integrated with rosetta,
and i would like to know if there is a specific algebric library i should use?

Yigal.

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ddg_monomer mutations list: How to specify chain ID?

Category: 
Design

I want to use ddg_monomer with multiple simultaneous mutations. According to the documentation (https://www.rosettacommons.org/docs/latest/ddg-monomer.html) this requires a mutation file, instead of the resfile used by other applications.

However, in the example provided by the documentation, there is no use of a chain ID. My structure has multiple chains.

How can I specify a chain ID in the mutation file?

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Does a negative Rosetta dG imply a favorable process?

Category: 
Design

I know that Rosetta's energies are given in Rosetta Energy Units (REU), which are not real free energy units, but which sometimes correlate linearly with real free energies.

This means that if I have a bunch of dGs given by Rosetta, I compare them and interpret these values as Rosetta's telling me that this process is more favorable than this other process, and so on.

Post Situation: 

Instructing design scripts to use noncanonical AA instead of canonical

Category: 
Design

Hi, novice Rosetta user here (so apologies in advance for simple / silly questions).

I have small peptide ligands that I am using in standard grafting / design. This has been relatively straightforward. However, one monkey wrench I'd like to throw into the works would be for the design scripts to use a noncanonical amino acid instead of the corresponding canonical one. For example, instead of tyrosine, design interfaces assuming all tyrosines are phosphorylated, or alternatively, impose acetylation or methylation on certain residues.

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