[lammps-users] pizza.py question?


I have used lammps for a while. I download and
installed pizza.py to convert output.xyz file to a pdb
format file. But the pdb file which has been converted
didnot have a correct pdb format for pymol to read for
visualization purpose.

I have compared this pdb with standard pdb file. It
has format error. I wonder whether your group can
modify the pizza.py code so that it can create correct
format for pdb file.

Thank you!


I assume you mean convert a LAMMPS dump file
to a PDB file. Pizza.py will not convert xyz files
to PDBs.

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.