I want to use RosettaCM for density guided homology modeling. My structure contains taxol and other ligands: GTP and GDP, but my /rosetta/main/database/scoring/score_functions/facts contains params files for just GTP and GDP but not taxol. I atatched my taxol.pdb file for reference.
Thanks in advance.
Edit found this tutorial here: https://www.rosettacommons.org/demos/latest/tutorials/prepare_ligand/prepare_ligand_tutorial
| Attachment | Size |
|---|---|
 taxol.pdb | 5.76 KB |
Category:
Post Situation:
Rosetta comes with parameters for only a few common residues/small molecule ligands. Generally speaking, if you need to model with a small molecule, you'll need to create your own parameters. The tutorial which you found should take you through the process.
I'll also note that Rosetta now comes with the PDB chemical components dictionary, which allows Rosetta to autogenerate parameters for certain ligands - the ones which match the wwPDBs definition for their three letter code. This gives reasonable results for certain purposes, but you still may want to create your own parameters, as doing so gives you more control over how things are constructed, and most critically, allows you to create a rotamer library for the ligand. (The autogenerated parameters have a somewhat fixes internal orientation.)