Member Site Forums Rosetta 3 Rosetta 3 – Applications How to define pi-pi stacking in cst file? Reply To: How to define pi-pi stacking in cst file?


    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 (Don’t forget to manually add a pseudo bond from the virtual atom to the rest of the molecule – doesn’t do well with disconnected structures). For the element symbol, use “X” (special cased to be a “virtual” atom). 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 will typically rename the atoms, and Rosetta will get confused if the atom names don’t match up properly).