# Segmentation fault - While using ML based CHARMM force filed in gromacs

**URL:** https://gromacs.bioexcel.eu/t/segmentation-fault-while-using-ml-based-charmm-force-filed-in-gromacs/9885
**Category:** User discussions
**Created:** [August 14, 2024, 7:48pm UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-while-using-ml-based-charmm-force-filed-in-gromacs/9885 "2024-08-14T19:48:07Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![Priyanka\_yadav](https://avatars.discourse-cdn.com/v4/letter/p/a698b9/32.png) [@Priyanka\_yadav](https://gromacs.bioexcel.eu/u/Priyanka_yadav)
#### Post date: [August 14, 2024, 7:48pm UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-while-using-ml-based-charmm-force-filed-in-gromacs/9885/1 "2024-08-14T19:48:07Z")

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GROMACS version:2023.3  
GROMACS modification: Yes/No  
Here post your question

I have generated force field parameters for Benzene using Machine Learning in CHARMM (CGenFF format) and would like to use these parameters in GROMACS. I have added the bonded and nonbonded parameters in ffbonded.itp and ffnonbonded.itp, respectively, defined new atom types in atomtypes.atp, and added the topology in the cgenff.rtp file (with the BZN molecule type). Using cgenff\_charmm2gmx\_py3\_nx2.py, I was able to obtain bzn.top, bzn.itp, bzn.prm, and bzn\_ini.pdb files. I also generated a .gro file from bzn\_ini.pdb and solvated it. However, I encountered an issue during energy minimization:

Steepest Descents:  
Tolerance (Fmax) = 1.00000e+03  
Number of steps = 500000  
Segmentation fault

The program shows a segmentation fault and does not proceed further.  
I am attaching the relevant files, including bzn.itp, bzn.top, bzn.prm, and the solv.gro file.

[bzn.itp](https://drive.google.com/file/d/1D9771G8tHDYEQlSSMXk9FKxHkjJQFNxQ/view?usp=share_link)

[solv.gro]  
([solv.gro - Google Drive](https://drive.google.com/file/d/1wOpA0D_4oYU-u27FbLxbjEyF0HddFDyL/view?usp=share_link))

[bzn.top](https://drive.google.com/file/d/1OcxYF7gWycRQ5GaebpbwDV0ZLt85oQc8/view?usp=share_link)

[bzn.prm](https://drive.google.com/file/d/1ZH3hcVMMN5uabwfLCKpCk89thcy0_BVd/view?usp=share_link)

Can someone please help me to run this system.  
Thank You

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### Author: ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)
#### Post date: [August 20, 2024, 8:03am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-while-using-ml-based-charmm-force-filed-in-gromacs/9885/2 "2024-08-20T08:03:06Z")

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To reproduce this we would also the mdp file.

Can you post the standard error and standard output output?

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### Author: ![Priyanka\_yadav](https://avatars.discourse-cdn.com/v4/letter/p/a698b9/32.png) [@Priyanka\_yadav](https://gromacs.bioexcel.eu/u/Priyanka_yadav)
#### Post date: [August 30, 2024, 6:06am UTC](https://gromacs.bioexcel.eu/t/segmentation-fault-while-using-ml-based-charmm-force-filed-in-gromacs/9885/3 "2024-08-30T06:06:38Z")

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Dear @hess thank you for your response, Now the error has been resolved, at that time there was an issue in non bonded parameters.