1. Remove the loop region form your template.
2. Align the resulting template sequence with the same sequence but include the desired aa sequence. The alignment shoud look like this:
>template
AGF--------GHK
>target
AGFRRKTYDERLGHK
where RRKTYDERL is the sequence of the loop you want to model.
3. The use loopmodel build a new model and the loop conformation ab initio as in this example:
http://www.salilab.org/modeller/manual/node32.htmlhomology models will be named as "target.B9999*.pdb" whereas loop models "target.BL999*.pdb"
4. Create as much as possible loopmodels by setting the following parameters accordingly:
a.loop.starting_model
a.loop.ending_model
Also bear in mind that loop modeling works well for loop <12 aa. When the length exceed ~15 aa the reliability drops abruptly.
I would recommend searching the mailing list about loop modeling, this subject has been covered extensively in the past.
Thomas
PS: QUARK ab initio server has a new option that allows distance restraints. The problem is that it has a 200 aa limit and you have to include the surrounding environment of the loop in order to get an accurate prediction. I intend to try this option soon, so I'll keep you posted.