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Enzyme Design

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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fastdesign with constraints in RosettaScripts

Category: 
Enzyme Design

Hi,

I am using the FastDesign protocol in RosettaScripts to design some residues in the neighborhood of a ligand, specifically with constraints of N-O pair distance for NAD binding. 

I've added constraints for the two N-O pairs to be 3.0 and 3.3 angstroms each with harmonic function and sd of 0.5, but somehow the distances are not kept below ~4.0 at all. (I've just observed a structure with over 6.0 angstrom distances for the two pairs.

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Error when running enzyme_design tutorial

Category: 
Enzyme Design

I'm trying to run the enzyme_design tutorial from here:

 

https://www.rosettacommons.org/demos/latest/public/enzyme_design/README

The first 2 stages run fine, but when I run the Design step with the command:

$ROSETTA3/bin/enzyme_design.static.linuxgccrelease @rosetta_inputs/general_design.flags -s rosetta_inputs/UM_1_D41H116K189_1tml_11_mocktim_1.pdb -out:file:o scorefile.txt

The code crashed with the following error:

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How tu use Delta filter's relax_mover

Category: 
Enzyme Design

Hi,

I want to use https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Filters/filter_pages/DeltaFilter to calculate the difference in energy between wt and design. I think I have to use parameter relax_mover, but from the docs It is not clear what value to use. Does anyone have any experience with it?

Edit:

I dug into the source code and it appears that this should work:

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Re: Glutamic acid protonation

Category: 
Enzyme Design

Hi,

I am working on an enzyme design project for which I want one of the glutamic acid of the catalytic site to be protonated at OE2 position. I manually did that using schrodinger but when I prepared the structure using relax protocol, the glutamic acid becomes deprotonated. How, I can get a specific glutamic acid (For eg position 43) to be protonated specifically at OE2?

 

Thanks in advance for help

BH

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