GROMACS modification: No
I want to run a simulation for a protein - oligosaccharide complex. the oligosaccharide contains Beta-galactose and alpha- glucose. Now, can I run this complex using charmm36 ff; as I have seen top_all36_carb.rtf included. How will I define the glycosidic bond as because while running the first pdb2gmx command for .gro conversion it warned me about the 3 missing atoms.
Plz. guide me to a starting point so that I can be assured proper Hydrogen bond and angle topologies.
Anticipation from a naive user,