Dear All,
I wanted to make a model of human flavin-containing monooxydase 3 (FMO3) enzyme from the template FMO of *Saccharomyces pombe*. This enzyme has FAD residue that is important to the project I'm working on. But of all the model output, none came with this FAD residue.
I have tried simple usage automodelling provided in the manual and modelling with the guide from basic modelling tutorial (provided here: https://salilab.org/modeller/tutorial/basic.html). Lastly, I also have tried to use the script for including water molecules, HETATM residues, and hydrogen atoms to the model (described in here: https://salilab.org/modeller/manual/node18.html). The FAD residue was not present and I ran out of ideas on how to make this work. The FAD binding site is highly conserved in FMOs across species, so I don't see why it was excluded from the model.
In the last try the script gave me this:
read_pd_459W> Residue type FAD not recognized. 'automodel' model building will treat this residue as a rigid body. To use real parameters, add the residue type to ${LIB}/restyp.lib, its topology to ${LIB}/top_*.lib, and suitable forcefield parameters to ${LIB}/par.lib.
What should I do? Your inputs are so much wanted and appreciated
Fadhila Balqis Nurfitria