Metallicious

Metallicious (a playful combination of "metal" and "delicious") is an automated tool for creating force fields for metal-containing systems with a covalent model of the metal. By utilizing a library of templates, metallicious identifies the template that matches the metal site in the structure. It copies the bonded parameters from the template and performs charge redistribution to account for charge transfer. In cases where no suitable template is found, metallicious automatically performs parameterization.

Metallicious works with minimal user input, relying heavily on educated guesses, which may not always yield the expected results. Therefore, it is recommended to use the tool with caution.

Installation:

conda create --name metallicious python=3.9
conda activate metallicious
conda install rdkit autode psiresp mdanalysis networkx qcelemental==0.25.1 ambertools --channel conda-forge
pip install metallicious

Quick start

Parametrization of structure with coordinates saved as supramolecular_cage.xyz (*.xyz, *.pdb, *gro, etc. formats supported by MDAnalysis) with (nonbonded) force-field parameters supramolecular_cage.top (*top, *prmtop, etc. supported by ParmEd), which consists of two metals Pd2+ and Ru2+ and organic linkers, the input file might look like this:

from metallicious import supramolecular_structure
cage = supramolecular_structure('supramolecular_cage.xyz',
                                metal_charges={'Ru': 2, 'Pd':2 },
                                topol='supramolecular_cage.top',
                                vdw_type='uff')
cage.parametrize(out_coord='out.pdb', out_topol='out.top')

The supramolecular_structure function takes a coordination file, topology file , dictionary of metal ions along with their charge (and in case template parametrization is needed multiplicity) and type of Lennard-Jones library as an input.

See examples/ for more examples and metallicious.readthedocs.io for additional documentation.

Command line

It is also possible to use the metallicious just form command line. For example:

metallicious -f supramolecular_cage.xyz -vdw_type merz-tip3p -metal_and_charges Pd 2 Ru 2 -prepare_topol

For details, see:

metallicious -h