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Enzyme Design

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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Incorporating Rosetta Binary and Database to a Web Server Pipeline

Category: 
Design
Scoring
Enzyme Design
Constraints
Small Molecules
ROSIE

Our lab is planning to design a web server, and we would like to incorporate one of the binaries and the corresponding Rosetta database in our pipeline. 

We would like to incorporate Rosetta's supercharge binary (https://www.rosettacommons.org/docs/latest/application_documentation/design/supercharge) along with the corresponding common database in our web server as a component of our web server pipeline.

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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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Rosetta matching error

Category: 
Enzyme Design

I am working on ligand-based protein design by rosetta. I am getting a constant error on the rosetta matching algorithm to find possible binding sites in the protein molecule for the desired ligand. The error that I receive is "Cannot normalize xyzVector of length() zero". I tried running the script on different servers and multiple times but I get the same error everytime. What could possibly be going wrong?

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The question about  protonation of Rosetta

Category: 
Enzyme Design

I want to manually set  protonation of residues.

 I find  there are params in Rosetta database folder

 ASP_P1.params ASP_P2.params

GLU_P1.params GLU_P2.params

What are differences between ASP_P1.params and  ASP_P2.params,  and GLU_P1.params and GLU_P2.params ?

In additon,  HIS  has   two deprotonation states, HID and HIE, why there are only  one file HIS_P.params ?

The above problem pluzzes me for a long time,

 

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