# How to use a complex field to simulate sugars and glycosidases

**URL:** <https://gromacs.bioexcel.eu/t/how-to-use-a-complex-field-to-simulate-sugars-and-glycosidases/12868>\
**Category:** User discussions\
**Created:** [November 6, 2025, 3:16am UTC](https://gromacs.bioexcel.eu/t/how-to-use-a-complex-field-to-simulate-sugars-and-glycosidases/12868 "2025-11-06T03:16:43Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![wbj](https://avatars.discourse-cdn.com/v4/letter/w/e0b2c6/32.png) [@wbj](https://gromacs.bioexcel.eu/u/wbj)\
**Post date:** [November 6, 2025, 3:16am UTC](https://gromacs.bioexcel.eu/t/how-to-use-a-complex-field-to-simulate-sugars-and-glycosidases/12868/1 "2025-11-06T03:16:43Z")

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GROMACS version:  
GROMACS modification: Yes/No  
I would like to consult about performing a combined-force field simulation using GROMACS. Below is my approach (though I am unsure if it is entirely correct): I intend to use the GLYCAM force field for the oligosaccharide ligand and the AMBERff99SB force field for the glycosidase. I generated the oligosaccharide file using the CHARMM-GUI website, performed molecular docking with AutoDock Vina, then extracted the protein and oligosaccharide. I generated my oligosaccharide-TIP3P file via GLYCAM-Web, and subsequently used AmberTools to replace the coordinates of the docked oligosaccharide with those of the oligosaccharide generated from GLYCAM-Web, converting them into GRO and TOP files while modifying the small molecule files. However, when merging the protein-ligand files for simulation, a warning about duplicate atom definitions first appears. After ignoring this warning, during the NVT equilibration step, LINCS warnings arise, preventing further progress. Therefore, I would like to ask how I should revise my approach and steps to complete the combined-force field simulation. Thank you very much!

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