RosettaCommons / RosettaCommons/rosetta
Repeated RosettaDock crashes
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- Dominant language
- C++
- Stars
- 470
- Forks
- 169
- Avg merge
- 16d 23h
- Merged PRs (30d)
- 2
Description
I've been using RosettaDock 5.0 to determine a ligand ability to interact with a peptide. One of the ligands, phosophocholine (PC), appears to lead to normal docking procedures. Anything else that I tried consistently fails and sends out a crash log. I can't by eye determine the difference other than may of the other ligands are ring structures like inositol. I've even tried placing them in other starting locations and it still fails. I've got at least 3 different ring ligands that were all developed independently and I'm getting the same crashing. I'm attaching examples of the ones that worked and didn't work. I need help because this was specifically requested by a reviewer.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by downloading examples.docking.zip and reproducing the failures with RosettaDock 5.0, comparing the working PC case with the ring-ligand cases and their crash logs. Done should mean identifying a reproducible cause for the crashes and documenting or correcting the behavior.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- cpp
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100