You need to create a “DATA” file containing the starting conformation of the polymer (list of coordinates) as well as the list of bonded atom pairs. (For most people this also includes a list of 3-body angle, 4-body dihedral, and 4-body improper interactions. I realize you don’t need this yet.) The file format is explained here:
(there’s a small example here)
You can create the file yourself, or you can use one of these programs to build it for you:
Some DATA files (as in the above example) also include force-field parameters (“Pair Coeffs”, “Bond Coeffs”, “Angle Coeffs”, “Dihedral Coeffs”,…), but this is optional. Axel and I prefer putting the force-field parameters (the “Coeffs” in the example above) in a separate file. For this reason, both moltemplate and topotools (usually) omit the “Coeffs” from the data file and put them in a LAMMPS “input script” file which you can load independently of your starting conformation. (This way, you can tinker with the force field parameters without having to make a new “DATA” file each time.) This is optional.
Both moltemplate and topotools come with examples for building extremely simple polymers, like the one you are describing:
The procedure for building these polymers is explained in detail in chapter6 of the moltemplate manual
You can make a polymer which is straight and has no sidechains, if you omit the 2nd bead, and eliminate the rule for creating dihedral angle interactions (from “Dihedrals By Type” section of the the “force_field.lt” file for that example),
If you need to build a polymer that wraps around I curve, I recommend using “genpoly_lt.py” to build the .LT file which moltemplate will read (instead of the procedure shown above):
Hope this helps.
I tried “special_bonds lj 1 1 1” command
(This command is orthogonal to what you are trying to do.)