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PDB file showing error - missing heavyatom: OXT on residue LYS:CtermProteinFull 59

Submitted by intomybioverse on Wed, 2024-05-15 23:38
Category: 
Design

Hello everyone!

I am redesigning the specificity of a protein and make it interact with a DNA sequence. I am trying to run the RosettaDNA application program based on the demos. However, I am getting this error.

core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 1 atoms at position 89 in file myfile.pdb. Best match rsd_type:  ADE:UpperDNA
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue LYS:CtermProteinFull 59

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Rosetta 3 - Applications

Issues with rosetta numbering and keeping ligand when relaxing molecule.

Submitted by Wexter300 on Sun, 2024-04-28 14:37
Category: 
Design
[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:52:25.363712
[APPLICATION]: /pub/erikps/Rosetta3.14/main/source//bin/cartesian_ddg.static.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-39)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
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Rosetta 3 - General

Segmentation fault (core dumped) in rosettaDNA.static.linuxgccrelease

Submitted by intomybioverse on Sun, 2024-04-28 04:51
Category: 
Design

Hello everyone!

I am trying to redesign the protein-DNA interface to introduce novel interactions between a protein and a DNA molecule using the RosettaDNA application suite. 

I am getting this error after running the program. Can you help to fix this?

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Rosetta 3 - Applications

"Segmentation Fault" error occurred when Running a pilot job

Submitted by Cooben on Thu, 2024-04-18 19:47
Category: 
Design

Hello everyone! I'm trying to run a command in paper_interface_design_pilot_1000_commands.list generated in step 12 “Running a pilot job”
the commands are as follows:

cd /home/cooben/rosettatest/rosetta_src_2018.09.60072_bundle/main/source/paper_interface_design_pilot_1000/00000

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Rosetta 3 - Applications

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

Submitted by intomybioverse on Fri, 2024-03-15 06:44
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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Rosetta 3 - Applications

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