# CNT creation having more than 999 atoms

**URL:** https://gromacs.bioexcel.eu/t/cnt-creation-having-more-than-999-atoms/12619
**Category:** User discussions
**Tags:** pdb2gmx
**Created:** [September 8, 2025, 7:07am UTC](https://gromacs.bioexcel.eu/t/cnt-creation-having-more-than-999-atoms/12619 "2025-09-08T07:07:39Z")
**Posts on this page:** 4
**Page:** 1

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### Author: ![akshayani](https://avatars.discourse-cdn.com/v4/letter/a/db5fbb/32.png) [@akshayani](https://gromacs.bioexcel.eu/u/akshayani)
#### Post date: [September 8, 2025, 7:07am UTC](https://gromacs.bioexcel.eu/t/cnt-creation-having-more-than-999-atoms/12619/1 "2025-09-08T07:07:39Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Hello,  
I’m facing an issue while creating a CNT with more than 999 atoms. Since the PDB format restricts the atom name/serial number field to 4 characters, once it goes beyond C999, the numbering gets truncated and random values are assigned. This is causing errors. Can anyone suggest a solution for handling CNT structures with more than 999 atoms?

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<div class="post-metadata">

### 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: [September 16, 2025, 7:43am UTC](https://gromacs.bioexcel.eu/t/cnt-creation-having-more-than-999-atoms/12619/2 "2025-09-16T07:43:51Z")

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Only print the last three digits of the number.

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<div class="post-metadata">

### Author: ![akshayani](https://avatars.discourse-cdn.com/v4/letter/a/db5fbb/32.png) [@akshayani](https://gromacs.bioexcel.eu/u/akshayani)
#### Post date: [September 19, 2025, 4:13am UTC](https://gromacs.bioexcel.eu/t/cnt-creation-having-more-than-999-atoms/12619/3 "2025-09-19T04:13:06Z")

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But the sequence will repeat. We need to have unique no for each atom.

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<div class="post-metadata">

### 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: [September 19, 2025, 6:38am UTC](https://gromacs.bioexcel.eu/t/cnt-creation-having-more-than-999-atoms/12619/4 "2025-09-19T06:38:06Z")

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Is it unclear what you are referring to. The atom number field has 5 digits, the residue number 4. None have only 3.

The atom numbers are ignored completely by GROMACS. Atoms are renumbered consecutively from 1. Residues are recognized by a change in residue number. Repeats are fine, as long as consecutive residues have different numbers.