I would be surprised if you get a reasonable model even if the symptom (messages) is cured. Perhaps try a different alignment, different templates, different RAND_SEED (to get a different starting model).
However, if you really want to cure the symptom: These warnings fortunately go to standard output so you could edit the mod4 script in $MODINSTALL/bin/mod4 from
/usr/local/bin/modeller4/bin/${EXECUTABLE} $STEERF > $LOGF
to
/usr/local/bin/modeller4/bin/${EXECUTABLE} $STEERF | grep -v 'chkder___W' > $LOGF
I hope this helps.
Best, Andrej
szia@hanga.enzim.hu wrote: > > Hi, > > My log file from modeller is full of messages like these ones: > > chkder___W> DVX(i) out of bounds: 1742 1742Infinity > chkder___W> DVX(i) out of bounds: 1743 1743Infinity > chkder___W> DVY(i) out of bounds: 1744 1744Infinity > > The log file grows extremely fast. I stopped the program when the log file > was 182 megabytes big. > > With a smaller protein, these warnings do not appear. What could be wrong? > How can I switch off these warnings, possibly not interfering with other > warnings? > > Best, > > Andras Szilagyi (szia@enzim.hu) > Institute of Enzymology, Hungarian Academy of Sciences > Karolina ut 29., H-1113 Budapest, HUNGARY > Fax: +36 1 166 5465, phone: +36 1 166 5633
-- Andrej Sali, Assistant Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali@rockvax.rockefeller.edu; http://salilab.org