no - LAMMPS does not include a molecular builder.
Many other such codes exist, including other MD
codes (which can dump formats that can be
converted to LAMMPS formats), or PackMol.
It sounds like you have a PDB file with multiple biomolecules, and you
want to solvate it and automatically generate a LAMMPS data file with
the force-field parameters chosen automatically. For this kind of
all-atom system, more specialized codes like AMBER, NAMD, GROMACS (or
CHARMM) are designed for exactly this kind of all-atom simulation.
(You must choose the forcefield you want to use carefully.)
If you want to use LAMMPS you have access to software which can
generate input files for AMBER CHARMM, AMBER or Materials Studio.
Once you have these files there are scripts which can convert these
files into LAMMPS data format (ch2lmp, amber2lmp, msi2lmp). They are
Also check the other tools in that list. Be warned that some of these
tools (amber2lmp) are no longer maintained and may have bugs.
If you want to have more control over how the DATA file is built, then
have a look at moltemplate, topotools, and packmol:
Moltemplate is a general molecule builder designed specifically for LAMMPS:
Moltemplate is useful when you have mixtures of molecules containing
many copies of the same molecule. Because it was designed for
building coarse-grained molecules, the user has control (and the
responsibility) to specify the atom coordinates and the bonds between
atoms for every molecule type. Moltemplate will do the rest. Because
using moltemplate requires some manual labor, if you are looking for a
black-box program to automatically convert PDB files into LAMMPS data
files, this is not it. You must be familiar with LAMMPS data file
format to use moltemplate. (Once you are, using moltemplate should
not be difficult.) The moltemplate program needs better
documentation, but I am working on that. There are several examples
on the main web page and more bundled in the download. (Feel free to
email questions about it if you get stuck using it.)
Axel's "topotools", (which is a VMD plugin) can be used to create a
LAMMPS data file from the information stored in a PDB file.
Like moltemplate, this process is not fully automated.
The two programs are complementary. Moltemplate has a utility
(nbody_by_type.py) which can be used to automatically generate angle,
dihedral, and improper interactions between atoms which may be omitted
by topotools. Topotools has many utilities, and can create PSF files
to visualize LAMMPS trajectories in VMD.
Packmol is a powerful tool for generating atomic coordinates (and the
developers are nice). You can use it to generate atomic coordinates,
and use moltemplate or topotools to use the coordinates to build a
LAMMPS data file.
(Also, for simple chain-like polymers, pizza.py has a tool for
generating them: http://pizza.sandia.gov/doc/chain.html. But this
does not sound like the system you described.)
I hope this helps.
Feel free to post about any tools I left out.
Steve, are you willing to list moltemplate and topotools in the
lammps documentation in the "Additional Tools" section? These are
massive programs designed specifically for LAMMPS.
If not that section can you mention them somewhere in the lammps
documentation? (Although packmol was not designed specifically for
lammps, it is useful too.)