# Question about entry not found in rtp file

**URL:** https://gromacs.bioexcel.eu/t/question-about-entry-not-found-in-rtp-file/7477
**Category:** User discussions
**Created:** [October 26, 2023, 1:42pm UTC](https://gromacs.bioexcel.eu/t/question-about-entry-not-found-in-rtp-file/7477 "2023-10-26T13:42:37Z")
**Posts on this page:** 3
**Page:** 1

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### Author: ![schief](https://avatars.discourse-cdn.com/v4/letter/s/bc79bd/32.png) [@schief](https://gromacs.bioexcel.eu/u/schief)
#### Post date: [October 26, 2023, 1:42pm UTC](https://gromacs.bioexcel.eu/t/question-about-entry-not-found-in-rtp-file/7477/1 "2023-10-26T13:42:37Z")

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GROMACS version: version 2022.2-conda\_forge  
GROMACS modification: No

Dear community,  
I am trying to prepare a protein DNA complex with pdb2gmx (forcefields: AMBER99SB-ILDN protein, nucleic AMBER94) but failing with the fatal error:

Atom P in residue DA 734 was not found in rtp entry DA5 with 30 atoms  
while sorting atoms.

However, the dna.rtp file contains a proper DA entry with an entry for atom type “P”. Why is pdb2gmx is checking in entry DA5 instead of DA?

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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 27, 2023, 3:41am UTC](https://gromacs.bioexcel.eu/t/question-about-entry-not-found-in-rtp-file/7477/2 "2023-10-27T03:41:21Z")

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It is detecting this particular DA residue to be the 5’-terminus of a chain, hence it is applying DA5.

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<div class="post-metadata">

### Author: ![schief](https://avatars.discourse-cdn.com/v4/letter/s/bc79bd/32.png) [@schief](https://gromacs.bioexcel.eu/u/schief)
#### Post date: [October 27, 2023, 6:24am UTC](https://gromacs.bioexcel.eu/t/question-about-entry-not-found-in-rtp-file/7477/3 "2023-10-27T06:24:18Z")

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OK, this makes sense. Thanks for your fast reply.