# Problem in generation of the topology and .gro file

**URL:** <https://gromacs.bioexcel.eu/t/problem-in-generation-of-the-topology-and-gro-file/10944>\
**Category:** User discussions\
**Created:** [January 6, 2025, 6:59am UTC](https://gromacs.bioexcel.eu/t/problem-in-generation-of-the-topology-and-gro-file/10944 "2025-01-06T06:59:52Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![LIKITHA](https://avatars.discourse-cdn.com/v4/letter/l/2acd7d/32.png) [@LIKITHA](https://gromacs.bioexcel.eu/u/LIKITHA)\
**Post date:** [January 6, 2025, 6:59am UTC](https://gromacs.bioexcel.eu/t/problem-in-generation-of-the-topology-and-gro-file/10944/1 "2025-01-06T06:59:52Z")

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GROMACS version: gromacs-2022.2

When I run the gromacs commands, The topology generation is not happening and the job is getting aborted. Please help me to fix this issue.  
I am attaching the pdb file along. I am using the charmm36 forcefield.  
[file.txt](https://gromacs.bioexcel.eu/uploads/short-url/zd02z2kslo4SuleBPwzj7QRjFbV.txt) (159.1 KB)

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [January 7, 2025, 8:26am UTC](https://gromacs.bioexcel.eu/t/problem-in-generation-of-the-topology-and-gro-file/10944/2 "2025-01-07T08:26:11Z")

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I don’t think anyone will be able to help you without more information. What goes wrong?

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**Author:** ![LIKITHA](https://avatars.discourse-cdn.com/v4/letter/l/2acd7d/32.png) [@LIKITHA](https://gromacs.bioexcel.eu/u/LIKITHA)\
**Post date:** [January 7, 2025, 10:56am UTC](https://gromacs.bioexcel.eu/t/problem-in-generation-of-the-topology-and-gro-file/10944/3 "2025-01-07T10:56:26Z")

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The topology file is not being generated.(file.top)  
the file is created but it’s empty and thus the further steps cannot run.

command line : gmx\_mpi pdb2gmx -f $NAME.pdb -o $NAME.gro -p $NAME.top -ignh -water tip3p -ff charmm36-jul2022

Any other information needed, please let me know

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [January 7, 2025, 10:57am UTC](https://gromacs.bioexcel.eu/t/problem-in-generation-of-the-topology-and-gro-file/10944/4 "2025-01-07T10:57:52Z")

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I guess you get error messages, right?

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<div class="post-metadata">

**Author:** ![LIKITHA](https://avatars.discourse-cdn.com/v4/letter/l/2acd7d/32.png) [@LIKITHA](https://gromacs.bioexcel.eu/u/LIKITHA)\
**Post date:** [January 7, 2025, 10:58am UTC](https://gromacs.bioexcel.eu/t/problem-in-generation-of-the-topology-and-gro-file/10944/5 "2025-01-07T10:58:20Z")

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yes, i do.

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [January 7, 2025, 10:59am UTC](https://gromacs.bioexcel.eu/t/problem-in-generation-of-the-topology-and-gro-file/10944/6 "2025-01-07T10:59:21Z")

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They should say what the problem is. What do they say?

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**Author:** ![LIKITHA](https://avatars.discourse-cdn.com/v4/letter/l/2acd7d/32.png) [@LIKITHA](https://gromacs.bioexcel.eu/u/LIKITHA)\
**Post date:** [January 8, 2025, 9:10am UTC](https://gromacs.bioexcel.eu/t/problem-in-generation-of-the-topology-and-gro-file/10944/7 "2025-01-08T09:10:31Z")

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![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/8/8411602ae8bccaa594a04a3d00a2c1add599072b.png)

Something like this…

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [January 8, 2025, 9:18am UTC](https://gromacs.bioexcel.eu/t/problem-in-generation-of-the-topology-and-gro-file/10944/8 "2025-01-08T09:18:26Z")

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You need to make sure that your atoms are named correctly according to the topology database entries. There doesn’t seem to be a `CG2` atom in residue 5 (THR) in your input file.

See if [Residue mapped into topology database but atom name not found in file? - #10 by amei](https://gromacs.bioexcel.eu/t/residue-mapped-into-topology-database-but-atom-name-not-found-in-file/3675/10) or [Fatal error: Residue 1 named GLN of a molecule in the input file was mapped to an entry in the topol](https://gromacs.bioexcel.eu/t/fatal-error-residue-1-named-gln-of-a-molecule-in-the-input-file-was-mapped-to-an-entry-in-the-topol/751) helps.