# Atom OXT in residue DG 1 was not found in rtp entry DG5 with 31 atoms while sorting atoms **URL:** \ **Category:** User discussions\ **Created:** [November 29, 2020, 8:01am UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164 "2020-11-29T08:01:36Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![imrbay](https://avatars.discourse-cdn.com/v4/letter/i/67e7ee/32.png) [@imrbay](https://gromacs.bioexcel.eu/u/imrbay)\ **Post date:** [November 29, 2020, 8:01am UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/1 "2020-11-29T08:01:36Z")
Brief description of tools/files: my pdb file consist of dna sequence.When I given the command …pdb2gmx -f … -o … -p … -ignh I gate the following error Atom OXT in residue DG 1 was not found in rtp entry DG5 with 31 atoms while sorting atoms.before this error,I used dna.rtp from amber03.ff I renamed all the atoms.But I still get these error.How to fix Link: Contact person (name and email address): How the work has been tested/reviewed: ---
**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:** [November 30, 2020, 5:29pm UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/2 "2020-11-30T17:29:05Z")
It seems that `pdb2gmx` is interpreting your DNA as a protein residue and trying to apply a C-terminal patch to it. Make sure your input PDB file has appropriate chain identifiers or `TER` delimiters. Also note that the nucleic acid parameters within amber03.ff are from AMBER94 and are entirely unsuitable for modern MD simulations… ---
**Author:** ![gongrehk](https://avatars.discourse-cdn.com/v4/letter/g/b5ac83/32.png) [@gongrehk](https://gromacs.bioexcel.eu/u/gongrehk)\ **Post date:** [March 18, 2021, 8:41am UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/3 "2021-03-18T08:41:15Z")
Hi! To put several lysozyme molecules in one box, I packed them by Packmol, then encountered the similiar problem when using ‘gmx pdb2gmx’ to generate the top file. **fatal error: Atom OXT in residue LEU 129 was not found in rtp enty LEU with 19 atoms while sorting atoms.** I cheched the file ‘aminoacids.rtp’ and the atom OXT doesn’t exist. If deleting this line in PDB, GROMACS could proceed but it wolud also perceive these proteins as a large protein at the same time.This is not rational, right?Do you have any idea to solve this? I also tried to put a `TER` delimiter manually right below the last line of each lysozyme(ATOM 1001 OXT LEU A 129), then ‘gmx pdb2gmx’ worked but it seemed that GROMACS just perceived these proteins as individual sidechains, as shown in the last part of top file(see below).I wonder if it is okay to proceed the MD with this config? [molecules] ; Compound #mols Protein\_chain\_A 1 Protein\_chain\_A2 1 Protein\_chain\_A3 1 Protein\_chain\_A4 1 Protein\_chain\_A5 1 Protein\_chain\_A6 1 Protein\_chain\_A7 1 Protein\_chain\_A8 1 Protein\_chain\_A9 1 Protein\_chain\_A10 1 Protein\_chain\_A11 1 Protein\_chain\_A12 1 Thaks very much for your time! ---
**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:** [March 18, 2021, 1:53pm UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/4 "2021-03-18T13:53:44Z")
The output is fine. If `pdb2gmx` writes the topology, that means everything worked, even if the screen output was a little loud and noisy. ---
**Author:** ![gongrehk](https://avatars.discourse-cdn.com/v4/letter/g/b5ac83/32.png) [@gongrehk](https://gromacs.bioexcel.eu/u/gongrehk)\ **Post date:** [March 18, 2021, 2:03pm UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/5 "2021-03-18T14:03:56Z")
Yeah. Is there other ways to deal with this error? ---
**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:** [March 18, 2021, 2:15pm UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/6 "2021-03-18T14:15:14Z")
If `pdb2gmx` finished, you did not get an “error.” If you got an advisory note or warning, again that’s just `pdb2gmx` being noisy about its under-the-hood workings about patching terminal groups. It didn’t find OXT in a terminal residue, so what it’s actually doing is building one, the normal function of a C-terminal patch in the force field. ---
**Author:** ![gongrehk](https://avatars.discourse-cdn.com/v4/letter/g/b5ac83/32.png) [@gongrehk](https://gromacs.bioexcel.eu/u/gongrehk)\ **Post date:** [March 19, 2021, 1:36am UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/7 "2021-03-19T01:36:39Z")
I see! Thanks very much for your explanation! ---
**Author:** ![sparsh282](https://avatars.discourse-cdn.com/v4/letter/s/e47c2d/32.png) [@sparsh282](https://gromacs.bioexcel.eu/u/sparsh282)\ **Post date:** [May 10, 2021, 9:22pm UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/8 "2021-05-10T21:22:08Z")
@jalemkul I am trying to simulate ssDNA in water and had the same error pop up. I am using CHARMM27 forcefield for the DNA. Is that the correct forcefield package for nucleic acids? Thanks, Sparsh ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [May 11, 2021, 1:26pm UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/9 "2021-05-11T13:26:12Z")
Hi, What type of error do you refer to? Do you get error in pre-processing stage? Alessandra ---
**Author:** ![sparsh282](https://avatars.discourse-cdn.com/v4/letter/s/e47c2d/32.png) [@sparsh282](https://gromacs.bioexcel.eu/u/sparsh282)\ **Post date:** [May 12, 2021, 12:08am UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/10 "2021-05-12T00:08:57Z")
Hi Alessandra, I was using the pdb2gmx command to generate the .top , .itp , and .gro file for ssDNA. When I used the command I got the following error: Using the Charmm27 force field in directory ./charmm27.ff going to rename ./charmm27.ff/aminoacids.r2b Opening force field file ./charmm27.ff/aminoacids.r2b going to rename ./charmm27.ff/rna.r2b Opening force field file ./charmm27.ff/rna.r2b Reading DNA\_clean.pdb… Read ‘Unclassified’, 1537 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 48 residues with 1537 atoms chain #res #atoms 1 ‘A’ 48 1537 All occupancies are one Opening force field file ./charmm27.ff/atomtypes.atp Reading residue database… (Charmm27) Opening force field file ./charmm27.ff/aminoacids.rtp Opening force field file ./charmm27.ff/dna.rtp Opening force field file ./charmm27.ff/lipids.rtp Opening force field file ./charmm27.ff/rna.rtp Opening force field file ./charmm27.ff/aminoacids.hdb Opening force field file ./charmm27.ff/dna.hdb Opening force field file ./charmm27.ff/lipids.hdb Opening force field file ./charmm27.ff/rna.hdb Opening force field file ./charmm27.ff/aminoacids.n.tdb Opening force field file ./charmm27.ff/dna.n.tdb Opening force field file ./charmm27.ff/rna.n.tdb Opening force field file ./charmm27.ff/aminoacids.c.tdb Opening force field file ./charmm27.ff/dna.c.tdb Opening force field file ./charmm27.ff/rna.c.tdb Back Off! I just backed up topol.top to ./#topol.top.3# Processing chain 1 ‘A’ (1537 atoms, 48 residues) Identified residue G1 as a starting terminus. Identified residue C48 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Start terminus G-1: NH3+ End terminus C-48: COO- * * * Program: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1 Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1079) Fatal error: atom N not found in buiding block 1RG while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at [Errors - Gromacs](http://www.gromacs.org/Documentation/Errors) I am not sure how to fix this. Can you please help me with this. Thank you, Sparsh ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [May 13, 2021, 8:49am UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/11 "2021-05-13T08:49:09Z")
Hi, DNA residues in CHARMM force field are defined as DA, DT, DG, DC. From the error you get if looks like that the residues in your pdb file are labelled differently. Or? Pls note (when you change the resname) that pdb file as a fix format. Best regards Alessandra ---
**Author:** ![sparsh282](https://avatars.discourse-cdn.com/v4/letter/s/e47c2d/32.png) [@sparsh282](https://gromacs.bioexcel.eu/u/sparsh282)\ **Post date:** [May 15, 2021, 9:11pm UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/12 "2021-05-15T21:11:36Z")
Okay. Is there a more reliable source for generating pdb files for ssDNA? I am currently using [MC-Fold | MC-Sym](https://www.major.iric.ca/MC-Fold/) to generate pdb files Thank you once again for all the help. Regards, Sparsh ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [May 17, 2021, 7:43am UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/13 "2021-05-17T07:43:14Z")
Hi, Before, I have used 3DNA ([http://x3dna.org/](http://x3dna.org/)) to generate DNA structure. I think that MC-Fold is more RNA based. Best regards Alessandra ---
**Author:** ![Pooja](https://avatars.discourse-cdn.com/v4/letter/p/a5b964/32.png) [@Pooja](https://gromacs.bioexcel.eu/u/Pooja)\ **Post date:** [May 20, 2022, 2:39pm UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/14 "2022-05-20T14:39:09Z")
Hi, I am also facing the same error " **atom OXT in residue GLY326 was not found in rtp entry GLY with 7 atoms while sorting atoms"** while performing MD simulation using CHARMm36 forcefield for CDK9 protein which is having phosphorylated threonine residue at 186 position. I tried to replace OXT with OT2 in merged.c.tdp file still I am getting same error. anyone could you please help me in solving this error. Thank you in advance ---
**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:** [May 20, 2022, 3:07pm UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/15 "2022-05-20T15:07:58Z")
Either use the newest (July 2021) version of the force field, or you need to explicit set termini for all chains in the coordinate file. You cannot let `pdb2gmx` automatically choose termini for a mixed system with the way the force field files are organized in the older CHARMM36 ports. ---
**Author:** ![Pooja](https://avatars.discourse-cdn.com/v4/letter/p/a5b964/32.png) [@Pooja](https://gromacs.bioexcel.eu/u/Pooja)\ **Post date:** [May 21, 2022, 10:55am UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/16 "2022-05-21T10:55:06Z")
Thank you Justin for your valuable response now I am trying using july2021 version of CHARMm36 forcefield that error is resolved by modifying aminoacids.c.tdp file OXT atom with OT2 and in pdb file I replaced 1OCT and 2OCT atom with C and O respectively according to aminoacid.rtp file now I am getting another error- " **residue 1 named GLY of a molecule in the input file was mapped to an entry in topology database, but the atom N used in an interaction of type improper in that entry is not found in the input file".** I am new to GROMACS could you please suggest how to solve this error. ![Pdb](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/3/3dbdc33bc766ceead966708e16b417cc565f1bd2.png) ---
**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:** [May 21, 2022, 11:08am UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/17 "2022-05-21T11:08:47Z")
Residue 1 should not be assigned an improper - you need to make sure all your chains have distinct chain identifiers or are separated by TER cards. `pdb2gmx` for some reason thinks GLY1 is an internal residue. If the issue persists, please provide the full screen output of `pdb2gmx` (copy-paste, not screenshot, please) so we can diagnose further. ---
**Author:** ![Pooja](https://avatars.discourse-cdn.com/v4/letter/p/a5b964/32.png) [@Pooja](https://gromacs.bioexcel.eu/u/Pooja)\ **Post date:** [May 21, 2022, 2:09pm UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/18 "2022-05-21T14:09:55Z")
Hi I am still facing an issue so I am attaching the pdb file and the error I am getting after running pdb2gmx command. Please let me know which place I need to correct as I am new so dont have much knowledge about it. (Attachment pdb2gmx\_output.txt is missing) (Attachment 3BLR.pdb is missing) ---
**Author:** ![Pooja](https://avatars.discourse-cdn.com/v4/letter/p/a5b964/32.png) [@Pooja](https://gromacs.bioexcel.eu/u/Pooja)\ **Post date:** [May 21, 2022, 2:16pm UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/19 "2022-05-21T14:16:23Z")
Hi I am still facing an issue so I am attaching the pdb file and the error I am getting after running pdb2gmx command. Please let me know which place I need to correct as I am new so dont have much knowledge about it. [error.dat](https://gromacs.bioexcel.eu/uploads/short-url/gLd0p1HOgxBAYyjCyjIkFlDsPXH.dat) (9.9 KB) [protein.dat](https://gromacs.bioexcel.eu/uploads/short-url/6lE3emHNKtLdhDImDyTo3VddFh.dat) (419 KB) ---
**Author:** ![awacha](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/awacha/32/19_2.png) [@awacha](https://gromacs.bioexcel.eu/u/awacha)\ **Post date:** [May 23, 2022, 8:32am UTC](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164/20 "2022-05-23T08:32:28Z")
Hi Pooja, first of all, if you do not have a strong reason to do otherwise, I’d suggest to use a more recent version of GROMACS. Version 5.1.4 (released in Sep. 2016) is seriously outdated and unmaintained. I have tried to reproduce the error with GROMACS version 2021.5, using the FF release jul2021, with the fix to the COO- terminal ([described here](https://gromacs.bioexcel.eu/t/newest-charmm36-port-for-gromacs/868/7)) applied, and ‘THP1 Protein’ added in the residuetypes.dat file. This way pdb2gmx did not complain. For the sake of curiosity, I’m compiling version 5.1.4 to be able to reproduce the error, but seriously, consider using a more recent release of the code. Kind regards, Andras [Next page](https://gromacs.bioexcel.eu/t/atom-oxt-in-residue-dg-1-was-not-found-in-rtp-entry-dg5-with-31-atoms-while-sorting-atoms/1164.md?page=2)