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
-- Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt)