I have been using Topotools to generate my LAMMPS data file from an xyz
coordinate file but am having some problems.
When it writes the LAMMPS data file, all bond types are defined as type
1, regardless of which atoms are actually bonded together. However, when
it outputs the angles and dihedrals data, after I have used the
guessangles/dihedrals command, the angle/dihedral type are all numbered
uniquely, based on the which atoms form the angle/dihedral.
Is there anything I can do to get the bond type numbered correctly, so
different atom types which are bonded together are regarded as a
different type of bond.
School of Chemistry
University of Edinburgh
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