Hello everyone, I need to model neutral arginine (i.e. protonated H should not be with NH group) , But could not find any thing in charmm 36 force field for that. Any help is highly appreciated. Thanks in advance.
Description:(1) COO- and NH3+ should be COOH and NH2
(2) Generally Arginine remains in protonated form but I want to make neutral Arginine in which among three nitrogen in biguanidine group should contain hydrogen in such a way that it be neutral as a whole (i.e. one less hydrogen than protonated form).