Galactose -protein complex Dynamics

User discussions
1

GROMACS version:2019.6
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,
hemchandra

2

The residues supported in the force field are the individual monosaccharides. If you need a polymer of these, you will have to create your own residue definitions and modify atomic charges according to the patches listed in top_all36_carb.rtf in the CHARMM toppar distribution.