While doing protein minimization, I found that the terminal amino acids of gap (let say 80 and 110) have incomplete valency e.g. -C(O) and -NH instead of -C(O)O-/H and NH2/H+ as rosetta consider them very neighbours during renumbering step.
I tried modifying both residues (let say 80 and 110) in different protein visualization plateforma and fed to Rosetta, but it modifies them to -C(O) and -NH.
Could you suggest how to deal with it?
I hope I lucidly explianed my query, please let me know if I messed up my question.