On 8/11/14, 1:20 PM, flavio seixas wrote: > I was trying to make a restriction to generate a covalent bond between > NZ atom from Lisine with C4 atom of PLP cofator. > I search Manual and modeler-List to find some clues about how to do If you want to make a distance restraint (this is what your restraints file is trying to do) between those two atoms, then see http://salilab.org/modeller/9.14/manual/node28.html If you really want to make a covalent bond, you'll need to write a suitable CHARMM patch: see the CHARMM manual. You can then apply it like the existing DISU patch: http://salilab.org/modeller/9.14/manual/node24.html Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage