I sort of got Patches to work. Using the files from Ennio I did the following. 1. added CONECT information to 1bna_2n_modified.pdb, using pymol. Saved the file as 1bna_2n_modified2.pdb 2.Added a new atom type to the DNA_mod_CG.xml file <Type class="SP1" element="S" mass="32.06" name="DNA-S"/> 3. Mod...

Hi, I'm an openMM and MD novice, working on a similar problem. I have made an .xml file with the following <ForceField> <Patches> <Patch name="SP"> <RemoveAtom name="O1P" type="O"/> <AddAtom name="S01" type="S"/> <RemoveBond atomName1="O1P" atomName2="P"/> <AddBond atomName1="S01" atomName2="P"/> <A...