Dear Fadhila,As an alternative, you could also try modeling your protein with Structuropedia @ http://structuropedia.org.In your amino acid sequence to be modeled, simply place an X where the FAD ought to be.You can also email me the amino acid sequence that you wish to model--and I would be glad to feed it into Structuropedia at my end.
With warmest regards,
AMJAD FAROOQ PhD DIC | Associate ProfessorDept of Biochemistry, University of Miami School of MedicineLocation: Gautier Building, Suite 116Address: 1011 NW 13 ST, MIAMI, FL 33136, USALabpage: http://farooqlab.net | http://structuropedia.orgOn Wed, Nov 16, 2016 at 6:07 PM, Fadhila Balqis N <" target="_blank">.id > wrote:______________________________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 buildingwill 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 forcefieldparameters to ${LIB}/par.lib.What should I do?Your inputs are so much wanted and appreciatedFadhila Balqis Nurfitria_________________
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