RosettaCommons / RosettaCommons/rosetta
Peptide with a new crosslinker
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- Dominant language
- C++
- Stars
- 470
- Forks
- 169
- Avg merge
- 16d 23h
- Merged PRs (30d)
- 2
Description
I want to create a PDB structure of a peptide with a new crosslinker (the one in red) that does not have a params file in Rosetta. I used PyRosetta to create the structure of the peptide, and chemdraw to make the linker. Then I connected them in Avogadro. However, Rosetta could not read it, even when I generated the params file (mol_to_params). I want to know what protocol do we use to incorporate the new linker to a peptide structure so that Rosetta can understand. Also, for the linker, should I keep COOH group or just CO group and define the atom that forms the bond?
Thank you
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
Start by reviewing the reported PyRosetta, mol_to_params, ChemDraw, and Avogadro workflow and determine which Rosetta inputs are required for a peptide with a custom crosslinker. No repository file or test is named; done would be a validated protocol explaining the linker representation and the required params configuration.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- cpp, python
- Domain
- bioinformatics
- Issue type
- Documentation
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100