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
On 11/16/16 3:07 PM, Fadhila Balqis N wrote: > 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. ... > The FAD residue was > not present and I ran out of ideas on how to make this work.
Without seeing what you tried already, I'm not sure how to advise you.
> read_pd_459W> Residue type FAD not recognized. 'automodel' model building > will treat this residue as a rigid body.
That's what I would expect to see if you used '.' in the alignment for that residue. Generally it's easiest to treat nonstandard residues as rigid bodies.
Ben Webb, Modeller Caretaker
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 > >
I had a similar problem. But it was to generate a model that would include Zn ion and the Co Crystalized ligand. So I had to modify the scripts I was using. and I succeeded in transferring the both the ligand and the cofactor. If your problem is in this same line, then you might have to work on the script.
On 17 November 2016 at 16:50, Amjad Farooq amjad@farooqlab.net wrote:
> 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 >> >> > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > >
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Amjad Farooq -
Fadhila Balqis N -
Modeller Caretaker -
Veranso Conrad SIMOBEN