[lammps-users] pizza.py question?

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1

See the file examples/test_pdbfile.py. If you run

it, it creates tmp.single.pdb which I can read into

RasMol or PyMol. So it appears to be in a good

PDB format.

In my experience, I have found that the PDB files that pizza.py makes have numerical atom IDs where there would normally be the symbol of an element, and I have had to use awk or perl to fix that, at least so that the colors in AtomEye would display correctly.

2

The pdbfile tool in Pizza.py has 2 modes. If you provide
an existing PDB file as a template, then LAMMPS will
just replace the xyz coords of each atom with what
is in the dump file. Else LAMMPS builds the PDB
file from scratch and it has no PDB-style atom names,
like C2, so it just makes a very vanilla PDB file.

So if your template has symbols, the ones output by
pdbfile should retain those.

Steve