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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?

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Academic email recognition

Category: 
ROSIE

Hello, I am a postdoc at the Max Planck Istitute for Chemical Ecology and would to use ROSIE for acedemic purposes. My email adress scarr@ice.mpg.de is not recognized.

I posted this same request a few weeks ago and got no responce. Any help would be greatly apreaciated. Cheers

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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.

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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?

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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.

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Segmentation Fault

Category: 
Loop Modeling

Hello! I'm trying to run add some missing loop to my protein by appear segmentation fault as error.

Anyone have an idea to solve this issue?

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Stub Libraries for DockWithHotspotMover

Category: 
Docking

Hello!

I was a little bit confused about what exactly the stub libraries are and how we are supposed to generate them. From what I understand, they're simply just disembodied residues that we consider "important" to the interface in the docked complex. So, are the stub files just generated by taking a protein structure and deleting everything except for the hotspot residue, then saving that singular residue as a PDB file? Also, is it possible to assign hotspot residues to both chains that we are docking together?

Thank you so much.

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