Please report MODELLER bugs by e-mail to the MODELLER users list at modeller_usage@salilab.org. It is best if you e-mail an uuencoded compressed tar archive of the directory with all input and output files:
tar cvf name.tar ./directory_name compress name.tar uuencode name.tar.Z name.tar.Z > name.uue mail -s 'MODELLER bug' modeller_usage@salilab.org < name.uue
If the problem is not apparent in the log files, please include in the archive a README file with a short description of the problem.