In the example peptide, there are 2004 atoms, 1365 bonds, 786 angles … in data.peptide.
I want to know how they are got.By what software?
Many programs can produce molecular models: other MD codes, VMD,
the scripts in the lammps tools dir that convert from PDB to LAMMPS (for
example). As I recall that particular one was from a Monte Carlo builder
program for peptide chains, and then solvated with CHARMM.