Thank you for your suggestions !!
I'm looking for way to get bonds list using VMD or other software, but I don't know their format and meanings of numbers.
Topotools can create bonds automatically between pairs of atoms which
are sufficiently nearby:
Also, do you know the format of the full style atom style?
I have attached the "data.peptide" from the "examples/peptide"
directory that comes with the LAMMPS source code. It is a very good
example. (Note: I had to gzip it to reduce the file size below 200K.)
I also tried to use Moltemplate, but I usually use fortran, so I had no idea how to deal with python. I will install python 3 in my account bin directory.
cool. never a bad idea to have a modern version of python available.
(If you plan to use moltemplate, then nearly all of the moltemplate
examples use "atom_style full". An example of a molecule that uses
"atom_style full" in moltemplate format is shown here:
It is very similar to the LAMMPS format.)
data.peptide.gz (82.3 KB)