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

["Joaquim Rui Rodrigues" <>]

Dear Modellers,

I am trying to build some missing loops in a PDB structure with modeller 9v4. For this, I am using the script found 
in examples/automodel/model-loop-define.py  for which I only changed residue_range's, and alnfile, knowns and 
sequence. The protein is a dimer, and both subunits end with a Gly residue.
 
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

A related message in the archives suggests editing modlib/atmcls-melo.lib (http://www.salilab.org/archives/
modeller_usage/2004/msg00169.html). This file seems to be used for loop modelling, but not for DOPE 
evaluation, as suggested in the log file:
openf___224_> Open           ${LIB}/atmcls-mf

I have also tried to use the dope_loopmodel class, instead of loopmodel. Here, I get the same warnings for both 
stages (loop modelling and DOPE assessment).

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

Many thanks,
Rui Rodrigues




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