HI Emad, you do not specify what you want to achieve with the modification of your peptide. I would recommend that you rely on Chemistry, i.e. on chemical parameters on the constituent amino acids. No program will figure out what you have in mind.

I am also confused on the "sequence". If you have a peptide, i.e. a short sequence, you may want to modify a residue or a couple or residues more than modifying a "sequence"

Hi Emad, I agree with Rafael, you need to provide more information on what you are trying to do in order for anyone to give you an answer. 

Hi  Rafael Franco and  Michael J. Benedik,

Sorry I know it is a silly question but I need to know your theoretical method. When I have a peptide sequence counting from 40 amino acids.  which part shall I take if i need to take a 20 amino acids sequence? and in which place I should make the replace for the amino acid  to do i, i+4 or i, i+7 bridge?

There is no relevant theory here, without more information you are just going to be making a guess.