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Enzyme Design

Enzyme Design FlexBB Protocol Bug: DNA/RNA handling

Category: 
Enzyme Design

Hi Folks,

I've been playing with the enzyme design binary application using enzymes containing DNA or RNA in the pose. The FlexBB protocol can be activated by setting the flag '-enzdes:flexbb_protocol true'. If no loop file is provided via the flag '-enz_loops_file <file>' the default  protocol behavior is to iterate through the pose to identify flexible regions in the structure for loop design. I found that having either DNA /RNA  in the pose triggers the following error consistently after cst minimization. 

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The question about FavorNativeResidue

Category: 
Enzyme Design

 I  read the paper Rosetta and the Design of Ligand Binding Sites doi:10.1007/978-1-4939-3569-7_4.

 

then try to use  EnzRepackMinimize  to design the protein.

But FavorNativeResidue was set as 0.5-3.0, the mutant position numbers are same and there are too many mutant positions.

However, I use the PackRotamersMover  by changing  FavorNativeResidue and can get different mutant position numbers.

How can I solve it? Thanks.

 

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Adding bridged water interaction in constraint file

Category: 
Enzyme Design

Hi,

 

I am working on Rosetta Enzyme Design Application trying to design a protein with a particular ligand in desired geometry. I wanted to define a bridged hydrogen bond interaction between the carboxylate group on the ligand and the arginine residue in protein via water molecule.

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How to minimize only a few key residues' orientation

Category: 
Enzyme Design

Hi everyone,

I am currently checking mutations of some key residues in the substrate binding pocket. So far, I used pymol wizard to automatically iterate all 20 amino aicds mutations from position and then use rosetta minimizer to optimize the local energy. 

Since I only change a few residues of the protein, is there any ways that I can only minimize a few positions instead of minimization of whole protein?

 

Thanks,

Ronghai

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Consistent XYZvector length() zero failure in EnzDes

Category: 
Enzyme Design
Non-Canonical Peptides

So...a bunch of other posts says to just rerun it if Rosetta fails with "cannot normalize xyzVector of length() zero". But what if you DO get this error consistently across different runs with different seeds? Like, every time? Where should I start looking to even solve this problem? I'm running EnzDes in Rosetta 3.8 (working on updating to 3.10), and it fails here. I am using a NCAA and a water molecule in the active site. 

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Error in enzyme_design.default.linuxgccrelease: corrupted size vs. prev_size

Category: 
Design
Enzyme Design

Dear Rosetta Team,

I am trying to run enzyme design protocol on protein model with 2 Iron ions, 2 Ions, 1 molecule and 1 water molecule (!). Problem is it is getting core dump/segmentation fault each time I run it. After various code recompilations and printing the error I came came to know the error is at "EnzdesBaseProtocol::enzdes_pack(" in EnzdesBaseProtocol.cc.

code:

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Do Rosetta support hydroxide(OH-) and oxide(O2-) params?

Category: 
Enzyme Design
Small Molecules
Chemically Modified Residues

Hello All,

For one of my project I need to hydroxide (OH-) and oxide (O2-). EnzDes is failing to take it. 

Error: caught exceptionFile: src/numeric/xyzVector.hh:665Cannot normalize xyzVector of length() zero

Oxide Params
 

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Pyrosetta protocol to move protein-peptide docked complex closer to active site.

Category: 
Design
Enzyme Design

Hi,

I have a protein-peptide(15 a.a) system with alreaddy a good guess for the binding mode of the peptide. Now I want to move slightly the peptide to a more reactive conformation and design mutants in this reactive conformation.

The “enzdes” application with a constraint file would do exactly what I need but I think it was created for “protein-small ligand” systems and I cannot use it with a multiple residues ligand like my peptide.

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