# DNA in charmm36

**URL:** <https://gromacs.bioexcel.eu/t/dna-in-charmm36/10496>\
**Category:** User discussions\
**Created:** [November 6, 2024, 3:32pm UTC](https://gromacs.bioexcel.eu/t/dna-in-charmm36/10496 "2024-11-06T15:32:52Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![jacopo1](https://avatars.discourse-cdn.com/v4/letter/j/13edae/32.png) [@jacopo1](https://gromacs.bioexcel.eu/u/jacopo1)\
**Post date:** [November 6, 2024, 3:32pm UTC](https://gromacs.bioexcel.eu/t/dna-in-charmm36/10496/1 "2024-11-06T15:32:53Z")

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GROMACS version:  
GROMACS modification: Yes/No  
i’m facing a problem in creating topology for dna with charmm36. That’s what i got .  
Atom C7 in residue DT 2 was not found in rtp entry DT with 32 atoms  
while sorting atoms.Also by modifying C7 into C5M it doesn’t work.

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**Author:** ![milosz.wieczor](https://avatars.discourse-cdn.com/v4/letter/m/b19c9b/32.png) [@milosz.wieczor](https://gromacs.bioexcel.eu/u/milosz.wieczor)\
**Post date:** [November 7, 2024, 5:29pm UTC](https://gromacs.bioexcel.eu/t/dna-in-charmm36/10496/2 "2024-11-07T17:29:11Z")

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Hi Jacopo,

Indeed, C5M is Charmm36’s way of naming the methyl carbon in thymine. Did you get exactly the same error after the modification (`Atom C5M in residue DT 2 was not found...`)?

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**Author:** ![jacopo1](https://avatars.discourse-cdn.com/v4/letter/j/13edae/32.png) [@jacopo1](https://gromacs.bioexcel.eu/u/jacopo1)\
**Post date:** [November 8, 2024, 2:21pm UTC](https://gromacs.bioexcel.eu/t/dna-in-charmm36/10496/3 "2024-11-08T14:21:41Z")

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after a couple of attempts the command has worked properly.Thanks.