How to write an entire trajectory into a single PDB file?

I have a trajectory (few frames) that I want to stack together and build a single PDB. I thought either to use VMD or [MDAnalysis](https://www.mdanalysis.org/docs/documentation_pages/coordinates/PDB.html) library. 


With VMD if I do [`atomselect`](http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node108.html) it takes a frame identifier as an argument. With MDAnalysis I saw this:



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

```

However, I am not sure how to use it in a complete script. 





```
#!/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.


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