# Atom C7 in residue DT 3 was not found in rtp entry DT with 32 atoms while sorting atoms

**URL:** https://gromacs.bioexcel.eu/t/atom-c7-in-residue-dt-3-was-not-found-in-rtp-entry-dt-with-32-atoms-while-sorting-atoms/7280
**Category:** User discussions
**Created:** [September 27, 2023, 2:44pm UTC](https://gromacs.bioexcel.eu/t/atom-c7-in-residue-dt-3-was-not-found-in-rtp-entry-dt-with-32-atoms-while-sorting-atoms/7280 "2023-09-27T14:44:03Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![janviverma926](https://avatars.discourse-cdn.com/v4/letter/j/ecc23a/32.png) [@janviverma926](https://gromacs.bioexcel.eu/u/janviverma926)
#### Post date: [September 27, 2023, 2:44pm UTC](https://gromacs.bioexcel.eu/t/atom-c7-in-residue-dt-3-was-not-found-in-rtp-entry-dt-with-32-atoms-while-sorting-atoms/7280/1 "2023-09-27T14:44:03Z")

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Hello,

I am getting the following error during pdb2gmx.

Fatal error: Atom C7 in residue DT 3 was not found in rtp entry DT with 32 atoms while sorting atoms.  
while preparing topology file for DNA.

I checked the pdb file and ffopls.rtp file also.

jahanvi

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### Author: ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [October 4, 2023, 1:20pm UTC](https://gromacs.bioexcel.eu/t/atom-c7-in-residue-dt-3-was-not-found-in-rtp-entry-dt-with-32-atoms-while-sorting-atoms/7280/2 "2023-10-04T13:20:26Z")

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> [@janviverma926](#):
>
> I checked the pdb file and ffopls.rtp file also.

What did you find? Your PDB file names an atom in a way that is not consistent with what the force field expects.

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<div class="post-metadata">

### Author: ![janviverma926](https://avatars.discourse-cdn.com/v4/letter/j/ecc23a/32.png) [@janviverma926](https://gromacs.bioexcel.eu/u/janviverma926)
#### Post date: [October 11, 2023, 4:09pm UTC](https://gromacs.bioexcel.eu/t/atom-c7-in-residue-dt-3-was-not-found-in-rtp-entry-dt-with-32-atoms-while-sorting-atoms/7280/3 "2023-10-11T16:09:11Z")

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hello sir,

I appreciate your response and assistance.  
After thoroughly analysing the terminal error, I attempted to replace C7 with C5M within the topology file. this was successfully accomplished.  
Am I able to make this change?  
I have attached my PDB file link for your review and would appreciate your assistance in checking it.

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Jahanvi