I would like to relax some decoys with a small molecule, P6G, in a specific location, extracted from a homologous protein from PDB. For doing so, I have saved a PDB file with the protein as chain A and P6G as chain B. Rosetta does not recognize P6G as a residue, for obvious reasons.
Is there a straightforward way to run the relax protocol in this situation?
Have you already worked through the tutorial here?
Adapting that procedure is probably the best way to handle your P6G ligand.
Hope that helps!
It has worked. Just what I needed.
Assuming that A) your molecule is from a published PDB and B) you don't need the molecule itself to move internally, try https://www.rosettacommons.org/docs/wiki/build_documentation/Build-Documentation#setting-up-rosetta-3_obtaining-additional-files_pdb-chemical-components-dictionary
This loads the PDB-published dictionary of chemical entities as residues Rosetta can recognize.