OpenFreeEnergy / OpenFreeEnergy/openfe
Protein+cofactors+ligands
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 331
- Forks
- 56
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 13
Description
Dear openFE developers.
We are testing system that has a protein + constant cofactor + ligands (congeneric series)
As the cofactor is constant we are exporting along with the protein. When we run the calculation it gets an error and I think it is because we are not providing force field parameters for the cofactor. If we run the same calculation without cofactor it works. This is for an RBFE protocol.
Any help on how to setup properly this would be highly appreciated.
Best wishes,
Cesar
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 reproducing the RBFE calculation with the constant cofactor and inspect the reported error, comparing it with the working calculation without the cofactor. Review how the protein, cofactor, ligands, and force-field parameters are supplied; done means identifying the missing setup or documenting the supported procedure.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100