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

User discussions
1

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