Molecule topology files on the Automated Topology Builder (ATB) website

Dear LAMMPS users,

To facilitate the simulation of systems involving organic molecules using LAMMPS, the Automated Topology Builder (ATB; see now provides topology files for all molecules in a LAMMPS compatible format. The LAMMPS files are designed for use with the moltemplate program () that is distributed with LAMMPS in the tools directory. Moltemplate allows forcefield parameters and molecule template files to be combined to build complex systems, enabling a workflow similar to that used to build system topologies in biomolecular MD simulation packages (eg GROMOS, AMBER, CHARMM etc). The ATB provides molecular topology building block files for a wide variety of molecules (> 20,000 and growing) in a variety of formats. Files can be accessed by visiting . Molecules can be found using the internal search tools based on name or chemical formula and selecting from the list of results. Once on the page for the molecule of interest, you should select the tab “Molecular Dynamics (MD) Files”. You will then need to choose “LAMMPS” from the “Format” drop-down box. If a molecule does not exist in the database, it can be added by submitting a new molecule to be processed (instructions in the site FAQ). Instructions on how to use the template files to prepare LAMMPS input data and script files are included in the file headers, and the moltemplate manual will also be helpful.

For example, the files for toluene can be found here: . You will need to register on the site in order to download files. Access to the ATB is provided free for academic (non-commercial) use. Feedback on how these files could be improved is very welcome, as are reports of bugs or problems with the files.

Best regards,


That's great!
I don't know how I overlooked this post for so long.
People have been asking me for something like this for a while.

--- comments ---
It looks as though the moltemplate file for molecule in your example
(Toluene) contains all of the topology information for that molecule,
including a complete list of all of the angles, dihedrals, and
impropers for that molecule.

This is fine. That's probably the point of the ATB service.

However, if you are like, I can help you include all the rules for
generating this topology directly into the moltemplate force-field
file itself, so you can omit the from each of the molecule template
files, and make each of the molecule template files shorter. Some new
features were added to moltemplate in the last 3 months to make it
easier to store this kind of information in an .LT file. (You would
do this by adding "replace", "Data Angles By Type", "Data Dihedrals By
Type", and "Data Impropers By Type" sections to the
"" file.)

--- bribery ---
I have been soliciting help converting force fields, such as
GROMOS_54A7 into moltemplate format. If you'd like to share the
script you wrote to convert the GROMOS_54A7 force field into
moltemplate format, I'd be happy to include you as a coauthor in the
upcoming moltemplate paper.

Either way, ATB looks like a fantastic resource.