On Sat, Nov 13, 2004 at 08:59:46AM +0000, aseem mishra wrote: > i wish to model a peptide with few unnatural amino acids in it. > > can some one please suggest a way.

See the Modeller FAQs 16 and 17: http://salilab.org/modeller/FAQ.html#16

If the unnatural amino acids are similar enough to natural amino acids, then it's probably better to look at FAQ 17, and adapt the parameters from the defaults, or obtain them from another source.

Ben Webb, Modeller Caretaker