how to use pdb as a template for a command line calculation?

Hi,
Im trying to build a model but i need to add a PDB i have as a template. I don't know how to use it as a template for a command line calculation without alingment.

This is the format of my PDB file
ATOM 1 N GLU A 1 68.406 121.088 100.468 1.00 24.27 N
ATOM 2 CA GLU A 1 67.078 121.454 101.009 1.00 24.27 C
ATOM 3 CB GLU A 1 66.330 120.188 101.458 1.00 24.27 C

Thanks for your help!