RosettaModel blueprint for PyRosetta
Submitted by bbrown11 on Tue, 2015-03-03 13:53
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Design
Design a peptide linked to small molecule ligand
Submitted by shaunmk on Mon, 2015-03-02 09:05
Category:
Design
Hi everyone,
I'm trying to design a peptide that binds to an enzyme. The tricky bit is that the peptide needs to be "grown" off of one end of a small molecule ligand that should dock into the active site. The ligand in question has an amide group at one of the ends, and we want to add amino acids to it. It also has a chlorine atom (pdb file attached).
What would be the best way to proceed with this problem? I'm unsure of how to let Rosetta's pepspec application know that it can add amino acids at the amide group.
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Filter ddg_filter reports failure!
Submitted by deepanshuiitb on Fri, 2015-02-27 18:19
Category:
Design
Hi,
I am trying to design a higher affinity interface for my protein-protein heterodimeric complex.But I'm getting the error which says "ddg is 0.246217 failing".I'm using the script similar to minpac_optE_premin.xml in the interface_design_demo folder of rosetta_2015.05.57676.
I really need some help to make this work.
Thank you!
p.s- I'll provide any other information if you need
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Pmut_scan with symmetry
Submitted by felipet on Thu, 2015-02-05 08:53
Category:
Design
Symmetry
Dear developers
I am trying to use pmut_scan for a symmetric dimer. I don't know if this is possible but when I run it with a symmetry definition file the program crashes with the following message:
protocols.pmut_scan.PointMutScanDriver: mutation mutation_PDB_numbering average_ddG average_total_energy
terminate called after throwing an instance of 'std::bad_cast'
what(): std::bad_cast
Pmut_sym.sh: line 29: 678 Aborted (core dumped) pmut_scan_parallel.default.linuxgccrelease
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Is there a way to restrict memory usage of ddg_monomer?
Submitted by cossio on Fri, 2015-01-30 14:35
Category:
Design
Is there a way to restrict the RAM memory usage of ddg_monomer?
Say I want to restrict ddg_monomer's memory usage to 512 MB. Is it possible?
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Calculate_protein_protein_ddg
Submitted by kamau on Fri, 2015-01-30 11:27
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
Submitted by brspurri on Sat, 2015-01-24 12:39
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.
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How to output all iteration structures from ddg_monomer?
Submitted by cossio on Fri, 2014-12-26 13:40
Category:
Design
I am using the flags for the low resolution protocol as documented here (https://www.rosettacommons.org/docs/latest/ddg-monomer.html):
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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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algebric library for rosetta
Submitted by yigallah on Mon, 2014-12-15 08:46
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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