Dear Samuel, Thank you so much for the quick reply! I did try the Ntc module to stabilize the A-form geometry, but still the MDparam tends to make my duplex extended. It makes sense that we do not have any solvent molecules and counter ions, so modeling the highly charged molecule is going to be ver...

Dear Samuel, I have been using MacroMolecularBuilder to model a duplex structure of self-complementary RNA. My main goal is to calculate a bunch of 1H-1H distances of a typical A-form duplex that was used in my NMR experiments. Several programs, such as Avogadro and PyMOL, have an option to model nu...