Re: [modeller_usage] W> MODEL atom not classified: GLY:OXT GLY

[Modeller Caretaker <>]

Joaquim Rui Rodrigues wrote:
> I am getting this warning at the DOPE potential assessment:
>>> Model assessment by DOPE potential
> iatmcls_286W> MODEL atom not classified:  GLY:OXT  GLY
> iatmcls_286W> MODEL atom not classified:  GLY:OXT  GLY

That's fine - it just means that the DOPE potential has no parameters
for terminal oxygens. That's because no such atoms were included in the
training set for the potential. So these warnings are normal and are
nothing to worry about.

> A related message in the archives suggests editing modlib/atmcls-melo.lib (http://www.salilab.org/archives/
> modeller_usage/2004/msg00169.html).

No, that's for the older loop modeling potential, which *does* have
parameters for terminal oxygens. That mailing list post merely addressed
the change in PDB atom naming for terminal oxygen from OT1/OT2 to OXT.

> This file seems to be used for loop modelling, but not for DOPE 
> evaluation

Exactly - the older loop modeling potential is used only for loop
modeling. DOPE is used both for loop modeling and for model assessment.

> How can I avoid such messages? Should I somehow edit atmcls-mf.lib?

The warnings are normal, so there is nothing you need to do.

	Ben Webb, Modeller Caretaker
-- 
             http://www.salilab.org/modeller/
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