I have xyz positions of my atoms in a .txt file, how can I extract information about bonding using VMD?

I want to create a LAMMPS input file that contains not only the positions, but also information about the bonding of the structure.


1 Answer 1


This seems to be what the TopoTools plugin is used for. This has commands for manipulating bonds/angles/dihedrals in VMD and then writing the corresponding information to a LAMMPS input file.

  • $\begingroup$ Thank you Tyberius, I am using topotools to read the xyz data by command "mol new" and then using the command "retype bonds" to get the bonding structure but I get the error there are more than 12 bonds ... $\endgroup$ Apr 5, 2022 at 14:20
  • $\begingroup$ @DelaramNematollahi This thread seems to be related. It seems like for your molecule this is trying to add 12 bonds around a single atom (or possibly several atoms). VMD doesn't set a limit on the total number of bonds, but depending the on the compiled version, it typically doesn't allow more than 12 bonds around an atom. $\endgroup$
    – Tyberius
    Apr 5, 2022 at 14:26
  • $\begingroup$ thanks a lot. in my file I do not have any bonding . I just have the x y z positions of atoms. basically I am looking for a way to or a command that can create the bonds between nearest neighbours and give me the bond information $\endgroup$ Apr 5, 2022 at 19:05

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