Hi Peter, thanks again for the reply, I think this is the part which is not too clear... my understanding is that patches allow to define new Residues based on existing ones, so we don't have to redefine an entire new residue because of a single modification. So far so good.... But then it would be ...

Hi Peter, Thanks for the prompt replies... Unfortunately i still have some problem to have the modified version (PS) working... I built a small example where you can reproduce the problem... I attached two inputs, one working (with unmodified bases) and one not working with the PS substitution, here...

Hi, Relatively new user here, I have been using openMM with amber FF for both DNA and RNA without major problems but I am struggling to apply patches to run modified DNA/RNA sequences. I had a look around the forum and I have followed the instructions on this link, http://docs.openmm.org/latest/user...