# While adding the force field parameter in dna aptamer

**URL:** <https://gromacs.bioexcel.eu/t/while-adding-the-force-field-parameter-in-dna-aptamer/8799>\
**Category:** User discussions\
**Tags:** forcefield\
**Created:** [April 5, 2024, 10:03am UTC](https://gromacs.bioexcel.eu/t/while-adding-the-force-field-parameter-in-dna-aptamer/8799 "2024-04-05T10:03:27Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![kareena](https://avatars.discourse-cdn.com/v4/letter/k/85e7bf/32.png) [@kareena](https://gromacs.bioexcel.eu/u/kareena)\
**Post date:** [April 5, 2024, 10:03am UTC](https://gromacs.bioexcel.eu/t/while-adding-the-force-field-parameter-in-dna-aptamer/8799/1 "2024-04-05T10:03:27Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Here post your question  
getting these error after running this command - gmx pdb2gmx -f apt02.pdb -o output.gro -ignh  
Fatal error:`  
Atom O5\* in residue DA 1 was not found in rtp entry DA5 with 30 atoms  
while sorting atoms.

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**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\
**Post date:** [April 5, 2024, 8:37pm UTC](https://gromacs.bioexcel.eu/t/while-adding-the-force-field-parameter-in-dna-aptamer/8799/2 "2024-04-05T20:37:10Z")

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Which force field you are using? check the atom type in the respective files and match that with your pdb

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**Author:** ![kareena](https://avatars.discourse-cdn.com/v4/letter/k/85e7bf/32.png) [@kareena](https://gromacs.bioexcel.eu/u/kareena)\
**Post date:** [April 6, 2024, 8:28am UTC](https://gromacs.bioexcel.eu/t/while-adding-the-force-field-parameter-in-dna-aptamer/8799/3 "2024-04-06T08:28:10Z")

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I’m using AMBER99sb force field

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**Author:** ![Seyilaxa](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/seyilaxa/32/3136_2.png) [@Seyilaxa](https://gromacs.bioexcel.eu/u/Seyilaxa)\
**Post date:** [April 6, 2024, 8:57am UTC](https://gromacs.bioexcel.eu/t/while-adding-the-force-field-parameter-in-dna-aptamer/8799/4 "2024-04-06T08:57:58Z")

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The atom name " O5\* " is not defined in the residue DA of AMBER forcefield, which might need to be modified to " O5’ " in the .pdb file. You could check the dna.rtp file in the forcefield’s folder to look up the right atom name in the first column in [atom] part.

> [DA5]  
> [atoms]  
> H5T HO 0.44220 1  
> O5’ OH -0.63180 2  
> C5’ CI -0.00690 3  
> H5’1 H1 0.07540 4  
> H5’2 H1 0.07540 5  
> ……