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 Professor * Dept of Biochemistry, University of Miami School of Medicine Location: Gautier Building, Suite 116 Address: 1011 NW 13 ST, MIAMI, FL 33136, USA Contact: amjad@farooqlab.net | +1-305-243-2429 Labpage: http://farooqlab.net | http://structuropedia.org
On Wed, Nov 16, 2016 at 6:07 PM, Fadhila Balqis N < fadhila.balqis@student.uns.ac.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 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 > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >