From: Yann Claveau (
Date: Wed May 12 2021 - 03:37:29 CDT

Dear all,

I used topotools to convert a pdb file into lammps data. I would like to
know if it is possible to change the numbering of atoms in the lammps
data file.

Here is an example : Consider 3 atom type : H, O, Si.

I selected them using

    set selSi [atomselect top {name Si}]
    set selO  [atomselect top {name O}]
    set selH  [atomselect top {name H}]

Then, after analysis (topo retypebonds, topo guessangles, mol reanalyze
top) I created the lamms data file.

    topo writelammpsdata data.example

In this file, atoms are ordered alphabetically:

    1 H
    2 O
    3 Si

is it possible to change this order using topotools, for instance:

    1 Si
    2 H
    3 O

Thanks for your help,

Yann claveau, post-doc
Département Matériaux-Nanosciences
Bât. 11A, bureau 122,
Campus de Beaulieu
Institut de Physique de Rennes - UMR-CNRS 6251
Université de Rennes 1
35042 Rennes cedex FRANCE