# Generate topology file for glucose

**URL:** <https://gromacs.bioexcel.eu/t/generate-topology-file-for-glucose/7940>\
**Category:** User discussions\
**Tags:** forcefield\
**Created:** [December 29, 2023, 10:15am UTC](https://gromacs.bioexcel.eu/t/generate-topology-file-for-glucose/7940 "2023-12-29T10:15:45Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![horlust](https://avatars.discourse-cdn.com/v4/letter/h/b2d939/32.png) [@horlust](https://gromacs.bioexcel.eu/u/horlust)\
**Post date:** [December 29, 2023, 10:15am UTC](https://gromacs.bioexcel.eu/t/generate-topology-file-for-glucose/7940/1 "2023-12-29T10:15:45Z")

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GROMACS version: 2021.4-2  
GROMACS modification: No

Hello everyone!

I am fairly new to GROMACS. I’ve been able to successfully run simulations for some small molecules with the OPLS-AA force field. My problem has always been the generation of the topology files. Using pdb2gmx seems impossible for my molecules, so I have been using x2top. When x2top can’t do the work, normally because it can’t find a forcefield type for one or more atoms, I try this tool: [http://erg.biophys.msu.ru/tpp/](http://erg.biophys.msu.ru/tpp/), or this tool: [https://traken.chem.yale.edu/ligpargen/](https://traken.chem.yale.edu/ligpargen/)

So far so good. However, I am now trying to generate topology for a glucose molecule, and with x2top I get:

Generating bonds from distances…  
Can not find forcefield for atom C1-2 with 3 bonds

* * *

Program: gmx x2top, version 2021.4-Ubuntu-2021.4-2  
Source file: src/gromacs/gmxpreprocess/x2top.cpp (line 186)

Fatal error:  
Could only find a forcefield type for 23 out of 24 atoms

The tools that I’ve mentionned aren’t doing the job correctly this time. From what I could understand, the atom that x2top doesn’t seem to find is of type opls\_278. Isn’t there a way to make x2top work with this information? I mean, I don’t understand why x2top doesn’t find this atom type is defined in the ffnonbonded.itp file.

I might use these files to do the job: [https://atb.uq.edu.au/molecule.py?molid=22619#panel-md](https://atb.uq.edu.au/molecule.py?molid=22619#panel-md), but I wanted to use the OPLS-AA force field.

Thank you in advance for your answers, and I wish you all a happy new year!  
Best,  
Maria

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**Author:** ![rpsingh](https://avatars.discourse-cdn.com/v4/letter/r/c57346/32.png) [@rpsingh](https://gromacs.bioexcel.eu/u/rpsingh)\
**Post date:** [December 31, 2023, 5:46pm UTC](https://gromacs.bioexcel.eu/t/generate-topology-file-for-glucose/7940/2 "2023-12-31T17:46:42Z")

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Use CHARMM-GUI.

1. Use Ligand modeller module to get CHARMM36 files of glucose
2. Upload the files in the Force Field Converter module to convert to OPLS files

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**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\
**Post date:** [December 31, 2023, 6:13pm UTC](https://gromacs.bioexcel.eu/t/generate-topology-file-for-glucose/7940/3 "2023-12-31T18:13:05Z")

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> [@horlust](#):
>
> OPLS-AA force field

@horlust the server not providing you all the paremters for the atoms?

`https://traken.chem.yale.edu/ligpargen/oplsaam_gmx_tutorial.html`