I am trying to do some loop modeling calculations. I found that after creating the template pdb from the parent pdb and the zones file, there were no HB atoms corresponding to any residue. Is that normal?
When I model the loop I find that the output pdb has these HB atoms at weird positions. I have just outputted one structure for testing. Is this just a consequence of not outputting numerous structures ( will these HB atoms find their correct position on calculating several structures? Also, if a loop is one residue long, how do I define it in the loops file...for example if the parent and query proteins have the same sequence between residues 45-50 and 52-57, how should I incorporate the 51st residue as a loop (is writing LOOP 50 52 0.0 0.0 good enough?)
I am attaching my template pdb and outputted structure (as png and text files) for your convenience.