# Galactose -protein complex Dynamics

**URL:** <https://gromacs.bioexcel.eu/t/galactose-protein-complex-dynamics/1022>\
**Category:** User discussions\
**Created:** [October 30, 2020, 11:28am UTC](https://gromacs.bioexcel.eu/t/galactose-protein-complex-dynamics/1022 "2020-10-30T11:28:25Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Hemchandra](https://avatars.discourse-cdn.com/v4/letter/h/3da27b/32.png) [@Hemchandra](https://gromacs.bioexcel.eu/u/Hemchandra)\
**Post date:** [October 30, 2020, 11:28am UTC](https://gromacs.bioexcel.eu/t/galactose-protein-complex-dynamics/1022/1 "2020-10-30T11:28:25Z")

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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

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [November 2, 2020, 3:01pm UTC](https://gromacs.bioexcel.eu/t/galactose-protein-complex-dynamics/1022/2 "2020-11-02T15:01:12Z")

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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.