# Unable to generate topology for my ligand

**URL:** <https://gromacs.bioexcel.eu/t/unable-to-generate-topology-for-my-ligand/11437>\
**Category:** User discussions\
**Tags:** mdrun, simulation-setup\
**Created:** [February 1, 2025, 9:23am UTC](https://gromacs.bioexcel.eu/t/unable-to-generate-topology-for-my-ligand/11437 "2025-02-01T09:23:33Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![keinerfan](https://avatars.discourse-cdn.com/v4/letter/k/e495f1/32.png) [@keinerfan](https://gromacs.bioexcel.eu/u/keinerfan)\
**Post date:** [February 1, 2025, 9:23am UTC](https://gromacs.bioexcel.eu/t/unable-to-generate-topology-for-my-ligand/11437/1 "2025-02-01T09:23:33Z")

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Dear GROMACS Forum,

I am encountering issues with creating ligand topologies for my simulations. When I attempt to upload my ligands to generate parameters using CGENFF, I consistently receive errors. This issue occurs in most cases, and I have been unable to resolve it.

Additionally, I have used CHARMM-GUI to generate the ligand topology(using ligand reader and modeler) and included the itp in my topol.top file and the prm file in itp file of ligand( because whenever I included or did not included it in topol.top I got errors about improper dihedral) , but I am still facing errors when running the gmx grompp command. Here is the specific error message I receive:

gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr  
…  
WARNING: Too few parameters on line of [unl.prm] (source file: toppush.cpp)  
ERROR: Atoms in the .top are not numbered consecutively from 1

I have checked the generated topology and parameter files carefully, but I am still unable to resolve the warnings and the fatal error about atom numbering.

Could anyone provide guidance on how to fix this issue or recommend a troubleshooting step I might have missed?