Active site of a LPMO protein

This example is taken from a research project on the LPMP protein. The active site coordinates are taken from the Protein databank file with ID 5ACG

To calculate bond angle force field parameters:

For bonds...

seminario_ff -f model.fchk -s model.gro -b :1@N-:3@CU :1@ND1-:3@CU :2@NE2-:3@CU

...and for angles

seminario_ff -f model.fchk -s model.gro -a :1@CG-:1@ND1-:3@CU :1@CE1-:1@ND1-:3@CU

The atoms are specified as AMBER mask, see documentation for the parmed package and delimited by dashes. Any number of bonds and angles can be specified.