Reply To: How to define pi-pi stacking in cst file?

[Anonymous]

The easiest way to get the coordinates is to average the six coordinates of the carbon atoms in the aromatic ring you’re adding it to (that’s a simple sum-and-divide-by-six average, for each of X, Y and Z). You would then manually add this in as an extra atom to the mol/mol2 file that you feed to molfile_to_params.py (Don’t forget to manually add a pseudo bond from the virtual atom to the rest of the molecule – molfile_to_params.py doesn’t do well with disconnected structures). For the element symbol, use “X” (special cased to be a “virtual” atom). molfile_to_params.py will spit out a PDB file that you can concatenate onto your protein PDB (you should be doing this anyway, even without the virtual atoms, as molfile_to_params.py will typically rename the atoms, and Rosetta will get confused if the atom names don’t match up properly).