There are now two free molecule building programs written
specifically for LAMMPS:
--- moltemplate ---
http://www.moltemplate.org
--- topotools ---
http://sites.google.com/site/akohlmey/software/topotools
Moltemplate was designed for building coarse-grained biomolecular
models. Moltemplate can create both: lammps DATA files (containing
geometry and topology), and lammps INPUT scripts (containing
force-fields, fixes, and groups). Unlike files generated by other
conversion tools, moltemplate gives users access to all of the
force-fields available in LAMMPS. Users can save molecules in
moltemplate's compact, readable template file format (".LT"), and
share them with others. Molecules can be used as building blocks for
bigger molecules. "Canned" force-fields (such as Dreiding, GAFF,
TraPPE, and user creations) can (in principle) also be saved in this
format and applied to molecules later. (Unfortunately moltemplate
currently requires a lot of memory: a 300000 atom system requires ~6GB
of RAM.)
Topotools is a molecule builder which leverages the power of VMD
and TCL to create lammps DATA files and convert them to and from other
formats. Topotools has two components: a middleware script which can
extract and manipulate topology information, and several high-level
applications built on top of it, which, for example can enable it to
read/write data files, replicate and merge systems. Together with VMD,
topotools can infer topology from PDB files, PSF files, and atom pair
distances, solvate a protein. Additional features for coarse-grained
molecules are planned.
Both packages can infer angle, dihedral, and improper interactions
from bond topology. Both tools have commands to generate molecular
geometry.
Both programs can read coordinates from files generated by PACKMOL
http://www.ime.unicamp.br/~martinez/packmol/
...and other PDB file builders.
The two programs have complementary features. Files created in one
tool can be read by the other. Both programs are under active
development.
Thank you for your attention.
Hello.
Andrew