Creating Initial Configuration

With regards to that page, I used "Avogadro", to generate the polystyrene
molecule. However, the file was in pdb format. With a pdb-psf combo,
generating a LAMMPS data-file with VMD-topo tools gives me complete
information (bonds/dihedrals) everything. With only a pdb file as input,
topo tools with guess functions, is giving me incorrect guesses for
impropers and dihedrals. I do not know how to extract dihedral/improper and

this is why those are called "guesses". topotools offers you the
option to manually override the automatic guess and manually set
anything you like. the topotools tutorial sections on my homepage
explain in detail how things can be adjusted, but - as mentioned
before - they don't work as a black box, but require a good understand
of what you want to achieve. the same is true for andrew's

angle information from any file that "Avogadro" generates.

this is a question you have to ask the avogadro developers. certainly,
writing out a PDB file discards any such information, since that file
format does not have the ability to store this. you can't expect
information to magically re-appear after you discarded it.