Reply To: a trouble during floppytail modeling

I’ve made some posts on these boards about constraints before:

http://www.rosettacommons.org/node/2313

The documentation is pretty good:

http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/constraint_file.html

In FloppyTail, use a constraint file as described in that last link, with the cst_file and cst_weight options. Note that FloppyTail only applies constraints in centroid mode, so you have to use constraints between backbone atoms (or the centroid atoms, if you care to look them up).

If you’ve read that documentation and still have questions, feel free to ask them.