N.Arun Prasanna wrote: > i am facing a major problem. > Template details: > my template is a denova protein (PDB code: 1JY4). My main aim is to > impose D-Proline on my sequence. > when i aligned and ran iteration, it says protein structure not read in. > The convention they followed for D-Proline is DPR To get the best results, you will probably need to define topology for the D-proline residue - see the section in the FAQ. In your case, it should be straightforward, since it is so similar to regular proline (a Google search for "d-proline charmm topology" should find a suitable topology file for you). > i tried to change it to PRO in coordinate file since i need the > D-Proline coordinate, but it is still not working. That's a little vague - I suggest you look through the mailing list archives, since many people have had similar problems. See also http://salilab.org/modeller/FAQ.html#18 If you make no progress, others may be able to help you if you can post actual input files. Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage