Forcefield and topology generator based on atomipy

Upload a GRO, PDB, XYZ, or CIF file to process with the atomipy topology generator

Your file will be processed to assign atom types and generate topology files

Supported formats: .gro, .pdb, .xyz, .cif
Optional: Add H, remove overlapping sites, replicate the structure
Defaults: MINFF = 500 kJ/mol/rad2, CLAYFF = no angles.
If angles are enabled, M-O-H angle terms are set according to MINFF
Uncheck to only generate structure files and log files (faster processing).
Select at least one format if topology generation is enabled.
When checked, the topology files describe the full system. Uncheck to write topology files (.itp, .psf, .data) for the mineral framework only — any ions and water present are still written to the structure files (.gro, .pdb, .xyz) but excluded from the topology.
What can be processed:
  • System box size, volume and density from the input structure
  • Element assignment based on atoms and their neighbours
  • Bond and angle calculation with periodic boundary conditions
  • Forcefield atom type assignment (MINFF or CLAYFF)
  • Automatic charge assignment based on the selected forcefield
  • Generation of processed structure files (.gro, .pdb, .xyz)
  • Generation of topology files (.itp for GROMACS, .psf for CHARMM/NAMD, .data for LAMMPS)
  • Optional CIF import through GEMMI
  • Optional advanced preprocessing: overlap fusion, BVS-guided protonation, and structure replication
Input file requirements:
  • Note that MINFF only supports the elements H, O, Mg, Ca, Si, Al, Fe, Ti, Li, F
  • All structures must be chemically reasonable and contain the right number of elements, including H
  • PDB files must contain box dimensions in a CRYST1 record for proper periodic boundary handling
  • XYZ files must contain box dimensions on the second line after a # character (e.g., "# 10.0 10.0 10.0 90.0 90.0 90.0")
  • GRO files should follow standard GROMACS format with box dimensions on the last line
  • CIF input requires GEMMI to be installed on the web server
  • Bond detection relies on reasonable atomic positions and standard bond lengths
Beta Version Disclaimer

This is a beta version of atomipy and there is no guarantee that the output is correct. Users are responsible for verifying that the generated files are reasonable and suitable for their purposes. Use the generated files at your own risk.

Performance Note

The online server at topology.atomipy.io (also reachable via atomipy.io/topology) runs on a minimal cloud instance and is intended for quick testing and evaluation — not for large or time-critical jobs. The atomipy topology generator logic has successfully been tested with systems having 50,000 atoms, but please note that processing such large structures is slow and might take 10-15 minutes or more.

For faster local execution, download the packages from GitHub and run them on your own machine:

Both packages include example scripts (e.g. scripts/run_sys2minff.py, scripts/run_minff_atomi.py) showing how to build and process input files locally.