# Building Polysaccharide from monosachharide units

**URL:** <https://gromacs.bioexcel.eu/t/building-polysaccharide-from-monosachharide-units/357>\
**Category:** User discussions\
**Created:** [June 22, 2020, 7:49pm UTC](https://gromacs.bioexcel.eu/t/building-polysaccharide-from-monosachharide-units/357 "2020-06-22T19:49:05Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Anirban12](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/anirban12/32/495_2.png) [@Anirban12](https://gromacs.bioexcel.eu/u/Anirban12)\
**Post date:** [June 22, 2020, 7:49pm UTC](https://gromacs.bioexcel.eu/t/building-polysaccharide-from-monosachharide-units/357/1 "2020-06-22T19:49:05Z")

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GROMACS version: 2018.6  
GROMACS modification: No

Dear all,  
I am trying to simulate a polysaccharide. I have checked that its monomer topology is present in the .rtp file. How to build its topology? Furthermore when I tried pdb2gmx it showed that some atom is missing from pdb file.[As far as I understand this error is perhaps regarding the glycosidic bonds which is not recognized by pdb2gmx]. Thanks in advance.  
Anirban

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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:** [June 22, 2020, 8:01pm UTC](https://gromacs.bioexcel.eu/t/building-polysaccharide-from-monosachharide-units/357/2 "2020-06-22T20:01:28Z")

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> [@Anirban12](#):
>
> As far as I understand this error is perhaps regarding the glycosidic bonds which is not recognized by pdb2gmx

Please provide the actual error message so we can better diagnose and provide advice.

You will need to create terminal residue entries in the `.rtp` file for the reducing and non-reducing ends of the polysaccharide, and you should not apply terminal patching via `.tdb` entries, because those won’t be recognized for non-protein/non-nucleic acid species. See [http://www.gromacs.org/Documentation\_of\_outdated\_version/How-tos/Polymers](http://www.gromacs.org/Documentation_of_outdated_version/How-tos/Polymers) for general concepts of what to do.

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**Author:** ![Anirban12](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/anirban12/32/495_2.png) [@Anirban12](https://gromacs.bioexcel.eu/u/Anirban12)\
**Post date:** [June 23, 2020, 5:01am UTC](https://gromacs.bioexcel.eu/t/building-polysaccharide-from-monosachharide-units/357/3 "2020-06-23T05:01:31Z")

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![Screenshot from 2020-06-23 10-22-27](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/32dae8223ef7aa737823c05159c78e7784331275.png)

Thanks Justin @jalemkul . Here is the actual error message. BGLA and BGLN are two residues (from which I want to make my polymer) that are already present in the .rtp file.

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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:** [June 23, 2020, 3:28pm UTC](https://gromacs.bioexcel.eu/t/building-polysaccharide-from-monosachharide-units/357/4 "2020-06-23T15:28:09Z")

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Missing hydrogens can be rebuilt from an entry in the force field `.hdb` file. Other missing atoms (like O1) need to have their names corrected in your input coordinate file. All input atom names must match the force field’s expectations.

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**Author:** ![Anirban12](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/anirban12/32/495_2.png) [@Anirban12](https://gromacs.bioexcel.eu/u/Anirban12)\
**Post date:** [June 23, 2020, 5:27pm UTC](https://gromacs.bioexcel.eu/t/building-polysaccharide-from-monosachharide-units/357/5 "2020-06-23T17:27:40Z")

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Thank you so much.I shall look into these.  
Regards.  
-Anirban