[modeller_usage] How to override the build_seq() command in loopmodel class

I am having knots in my structure, same problem as this person had- http://salilab.org/archives/modeller_usage/2005/msg00394.html

I went through the manual but could not find any specific part where such instructions have been mentioned (althought they could have been in some section I have missed).

Can anyone please direct me to the appropriate resources to solve this problem?