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

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