Simple Forcefield Atom Type Assignment & Topology Generator

Upload a GRO, PDB, or XYZ file to process with atomipy

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

Supported formats: .gro, .pdb, .xyz (must contain box dimensions)
Uncheck to only generate structure files and log files (faster processing).
Select at least one format if topology generation is enabled.
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)
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
  • 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.