# Issues with Ligand Topology Creation Using CGENFF and CHARMM-GUI

**URL:** <https://gromacs.bioexcel.eu/t/issues-with-ligand-topology-creation-using-cgenff-and-charmm-gui/10932>\
**Category:** User discussions\
**Tags:** simulation-setup, topology\
**Created:** [January 2, 2025, 6:03pm UTC](https://gromacs.bioexcel.eu/t/issues-with-ligand-topology-creation-using-cgenff-and-charmm-gui/10932 "2025-01-02T18:03:50Z")\
**Posts on this page:** 3\
**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:** [January 2, 2025, 6:03pm UTC](https://gromacs.bioexcel.eu/t/issues-with-ligand-topology-creation-using-cgenff-and-charmm-gui/10932/1 "2025-01-02T18:03:50Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Here post your question

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? Any help or insight would be greatly appreciated.  
I have uploaded my topol.top, it file and prm file of my ligand  
[topol.txt](https://gromacs.bioexcel.eu/uploads/short-url/tWiJ9plX4H5L0zvj7GtmoRDpC2L.txt) (855 Bytes)  
[UNLitp.txt](https://gromacs.bioexcel.eu/uploads/short-url/8fpKMBsrIIiz2QefNMPkzDLUAjC.txt) (17.4 KB)  
[unlprm.txt](https://gromacs.bioexcel.eu/uploads/short-url/aFLUqQJsUaHj0Ulz7PfnjJ20YxX.txt) (11.4 KB)

Thank you in advance for your time and assistance!

Best regards,

Erfan

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**Author:** ![askforarun](https://avatars.discourse-cdn.com/v4/letter/a/c5a1d2/32.png) [@askforarun](https://gromacs.bioexcel.eu/u/askforarun)\
**Post date:** [January 2, 2025, 11:07pm UTC](https://gromacs.bioexcel.eu/t/issues-with-ligand-topology-creation-using-cgenff-and-charmm-gui/10932/2 "2025-01-02T23:07:50Z")

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Do you have the pdb file of the ligand ?

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<div class="post-metadata">

**Author:** ![keinerfan](https://avatars.discourse-cdn.com/v4/letter/k/e495f1/32.png) [@keinerfan](https://gromacs.bioexcel.eu/u/keinerfan)\
**Post date:** [January 7, 2025, 2:34pm UTC](https://gromacs.bioexcel.eu/t/issues-with-ligand-topology-creation-using-cgenff-and-charmm-gui/10932/3 "2025-01-07T14:34:42Z")

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yes please just change the txt format to ppdb ( I had to because site doesnt allow to upload any pdb format)  
[ligand2.txt](https://gromacs.bioexcel.eu/uploads/short-url/z5RRkzaSEiwsd52ozw2FcLHYbNK.txt) (4.6 KB)j