How to write an entire trajectory into a single PDB file?
#!/usr/bin/env python2

import MDAnalysis

# file formats are automatically deduced; this is a standard topology and binary
# (NetCDF) trajectory from AMBER
topology = 'peptide_1.prmtop'
trajectory = '02_peptide_1_equil_NVT.nc'
u = MDAnalysis.Universe(topology, trajectory)

with MDAnalysis.Writer("all.pdb", multiframe=True) as pdb:
    for ts in u.trajectory:
        pdb.write(u)


One thing that may be important: I see lots of warnings when trying to use Python 3, so 2.7 is probably better at this point.