First you have to create the PDB file of your peptide by any software like Avogadro. Then using PyMOL, you can calculate the distance in measurement wizard.

Thank you Anindyasundar for the answer.  I will try. 

One caveat to doing it this way is that it assumes a "linear" like peptide.  You could try MD simulations or NMR to help you get distance restraints for the peptide in order to understand if it has some sort of "preferred" orientation instead of random coil. 

Thank you for your answer Chad M Petit.