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?
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Hi Allan,
Have you already worked through the tutorial here?
https://www.rosettacommons.org/demos/latest/tutorials/prepare_ligand/prepare_ligand_tutorial
Adapting that procedure is probably the best way to handle your P6G ligand.
Hope that helps!
-Jonathan
Jonathan,
It has worked. Just what I needed.
Thank you.
Állan.
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.