Dear ResearcherGate community,

I created a Coarse Grained system composed of a glyco-protein using the MARTINI force field and GROMACS files. Both sugar and protein parameter files were created by hands individually with different molecular types (glycan parameters were obtained from the literature). However, for simulation purposes, I must connect them by covalent bonds by merging all molecules into the same molecular type. As you can see, doing it manually requires a lot of work (renumbering all atom indexes, for example). So, I'm looking for a simple way of merging all molecules into an unique molecular type using any tools available. Note, the glycans were not martnized and can not recognised by the universal force field. Could anyone help with this issue?

Any comments or suggestions are welcome!

Best!