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Post Situation: 

Error in score funtion "hack_elec 0.42"

Category: 
Docking

Hello everyone!

I am getting this following error when I am trying to run a rosettaDNA application program in which i want to change the specificity of a protein so that it binds to a target DNA. In most published articles, I have seen "hack_elec 0.42 " or similar values. However, it's not working in my case. Can you help me with this?

Post Situation: 

How to use rewrite_rosetta_script.py to update XML script file?

Category: 
Design

Hello!

I am trying to run the default XML script to change the specificity of a protein so that it binds to a DNA sequence of interest. For this I am referring to the book Redesigning the specificity of protein-DNA interactions with Rosetta

Thyme S, Baker D. Redesigning the specificity of protein-DNA interactions with Rosetta. Methods Mol Biol. 2014;1123:265-82. doi: 10.1007/978-1-62703-968-0_17. PMID: 24510272.

However I am getting the following error message.

Post Situation: 

several question in mpensemble dock

Category: 
Docking

Hey guys, I counterpart with problems as topic saying:

First, I want to use others computational results as reference to optimized docking option, so I have to relax them into same scorefunction, meanwhile relax the inputs which generate from different methods for better results and avoid disulfide bonds error due to different scorefunction, right?

Post Situation: 

Creation of crystal_complex.pdb for docking

Category: 
Docking

Hello all,

I have been trying to dock a library of ligands to a protein while following the Meiler lab tutorials. While I have been able to prepare most of the prerequisite files, I am unsure how I am supposed to obtain 'crystal_complex.pdb'. Trying to download the protein bound with a ligand .pdb file from the protein data bank and using that as my crystal_complex.pdb does not seem to work. While it seems that options.txt and dock.xml have been set up correctly, protein complex.pdb is the only thing preventing me from running the docking itself.

Post Situation: 

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