# Generating GROMACS Topology for a Head-to-Tail Cyclic Peptide Using CHARMM36m

**URL:** <https://gromacs.bioexcel.eu/t/generating-gromacs-topology-for-a-head-to-tail-cyclic-peptide-using-charmm36m/13773>\
**Category:** User discussions\
**Created:** [October 16, 2026, 7:36am UTC](https://gromacs.bioexcel.eu/t/generating-gromacs-topology-for-a-head-to-tail-cyclic-peptide-using-charmm36m/13773 "2026-10-16T07:36:03Z")\
**Posts on this page:** 1\
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**Author:** ![xlr8](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/xlr8/32/5163_2.png) [@xlr8](https://gromacs.bioexcel.eu/u/xlr8)\
**Post date:** [October 16, 2026, 7:36am UTC](https://gromacs.bioexcel.eu/t/generating-gromacs-topology-for-a-head-to-tail-cyclic-peptide-using-charmm36m/13773/1 "2026-10-16T07:36:03Z")

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GROMACS version:2025.4  
GROMACS modification: No  
Here post your question

Hello everyone,

I am working with a protein–cyclic peptide complex obtained through molecular docking. The cyclic peptide was generated by forming a head-to-tail peptide bond between the N- and C-termini, resulting in a closed cyclic structure.

I would like to perform molecular dynamics simulations of this complex using GROMACS with the **CHARMM36m force field**.

My main question is whether `gmx pdb2gmx` can correctly generate the topology for a head-to-tail cyclic peptide while preserving the N–C terminal connection, appropriate atom types, charges, and bonded parameters.

If `pdb2gmx` cannot handle this reliably, what is the recommended workflow for generating a topology for the cyclic peptide that is compatible with CHARMM36? Should I generate the protein and peptide topologies separately and then combine them, or is there a dedicated tool or protocol for parameterizing cyclic peptides?

Regards

Varun