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