Hello!
I want to use a molecule with retinal in Rosetta. I've read the documentation on this page
https://www.rosettacommons.org/demos/latest/public/design_with_ncaa/README
But I also wanted to ask if I can somehow use the retinal parametrisation I already have for namd. There it is written in the CHARMM Parameter File.
Thank you in advance,
Dmitrii.
Category:
Post Situation:
Sorry, Rosetta doesn't understand the CHARMM parameter format, and there isn't (to my knowledge) any way to directly convert between the two.
BTW, if your ligand is not polymeric (e.g. there's no covalent connection to other residues), you don't necessarily need to do the full NCAA ligand prep. Instead, you can do the bit simpler preparation that's used with ligand docking (see https://www.rosettacommons.org/docs/latest/rosetta_basics/preparation/preparing-ligands and https://www.rosettacommons.org/docs/latest/application_documentation/docking/ligand-dock ). The only tricky part is making a conformer library in SDF or Mol2 format, which you might already have from your CHARMM parameterization.