# 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:** 2
**Author:** ![Pooja](https://avatars.discourse-cdn.com/v4/letter/p/a5b964/32.png) [@Pooja](https://gromacs.bioexcel.eu/u/Pooja)\ **Post date:** [May 24, 2022, 2:42am 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/1164/21 "2022-05-24T02:42:31Z")
Hi Andras, Thank you for your valuable suggestion, now I am able to generate a topology file using an updated version of GROMACS with CHARMm36 force field according to your explanation. Please let me know if you can reproduce the error by using version 5.1.4 just for my knowledge. Thanks & Best Regards Pooja singh ---
**Author:** ![bjwiley23](https://avatars.discourse-cdn.com/v4/letter/b/c6cbf5/32.png) [@bjwiley23](https://gromacs.bioexcel.eu/u/bjwiley23)\ **Post date:** [September 21, 2022, 12:01pm 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/1164/22 "2022-09-21T12:01:11Z")
What if you input `-f file` is already a GROMACs .gro file, say you made it with CHARMM GUI and you want to run `pdb2gmx` on that \*.gro file with the toplogy .top and inlcudes .itp files to make vsites. There is no `TER` in .gro files so for this input for example 1068 is last residue of Protein\_chain\_A in `complex.gro`. ```auto 1068ASN O117492 -4.744 -0.953 -1.574 1068ASN O217493 -4.522 -0.983 -1.601 1GLU N17494 -4.693 -0.509 4.976 ``` running ```auto gmx pdb2gmx -f complex.gro -p topol.top -o test.gro -vsite hydrogens ``` gives the canonical ```auto Fatal error: Atom O1 in residue ASN 1068 was not found in rtp entry ASN with 14 atoms while sorting atoms. ``` Does recognition of chain terminators only work if input is in PDB format/is PDB file? And if so, how can you convert say a “multiple chain” .gro file back to a multiple chain PDB file? ---
**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:** [September 21, 2022, 3:27pm 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/1164/23 "2022-09-21T15:27:16Z")
The `.gro` format does not support any sort of chain identifiers, so `pdb2gmx` will fail for any input `.gro` file that has more than one chain. Use `.pdb` format in this instance, and make sure all chains are indicated by chain IDs or separated by TER. ---
**Author:** ![kyrstyno](https://avatars.discourse-cdn.com/v4/letter/k/d07c76/32.png) [@kyrstyno](https://gromacs.bioexcel.eu/u/kyrstyno)\ **Post date:** [September 23, 2022, 9:32pm 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/1164/24 "2022-09-23T21:32:09Z")
Hi, I have been running into errors trying to create a topology file for an .pdb file that I have. I am using GROMACS 2018 on a server computer and the CHARMM36 2021 force field. I have also tried using older force field releases from 2020, 2019, and 2017, but all of these generate the same error. gmx pdb2gmx -f equil\_Piezo1\_923.pdb -o equil\_1bar\_DV.pdb -p equil\_1bar\_DV.top -ff charmm36-jul2021 - I selected TIP3P\_CHARMM Program: gmx pdb2gmx, version 2018.1 Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 753) Fatal error: Atom OT1 in residue LEU 141 was not found in rtp entry LEU with 19 atoms while sorting atoms. Looking at my original pdb file, this particular LEU has 20 atoms with OT1 and OT2 at the terminus. ![Screen Shot 2022-09-23 at 5.27.11 PM](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/9/961cd4c64a4312e497f8678288bbc3604c513c9e.png). Inside aminoacids.rpt LEU is supposed to only have 19 atoms with an O as the terminus. ![Screen Shot 2022-09-23 at 5.31.12 PM](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/a/ad1e38658512b71e732ad403ae65d7917fcfc279.png) Is there a way to reconcile this? The atomistic pdb does not appear to have missing atoms. Thank you for any advice, Kyrstyn ---
**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:** [September 24, 2022, 1:51am 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/1164/25 "2022-09-24T01:51:09Z")
OT1 and OT2 refer to the carboxylate O atoms at the C-terminus. Your input coordinate file suggests that Leu141 is the C-terminal residue, but for some reason, `pdb2gmx` does not think it is. Please provide the full screen output of `pdb2gmx` so we can see what it is doing. ---
**Author:** ![kyrstyno](https://avatars.discourse-cdn.com/v4/letter/k/d07c76/32.png) [@kyrstyno](https://gromacs.bioexcel.eu/u/kyrstyno)\ **Post date:** [September 30, 2022, 8:43pm 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/1164/26 "2022-09-30T20:43:57Z")
Thank you. I have attached the full screen output of pdb2gmx in the following file. [output.log](https://gromacs.bioexcel.eu/uploads/short-url/f2tI7Y5xGtTAtlrhO8O44QSYGpO.log) (579.5 KB) ---
**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 1, 2022, 2:21am 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/1164/27 "2022-10-01T02:21:15Z")
```auto Warning: Residue POPC4681 in chain has different type ('Other') from residue LEU1 ('Protein'). This chain lacks identifiers, which makes it impossible to do strict classification of the start/end residues. Here we need to guess this residue should not be part of the chain and instead introduce a break, but that will be catastrophic if they should in fact be linked. Please check your structure, and add POPC to residuetypes.dat if this was not correct. ``` It appears you have a very complex, multi-component system that you’re trying to pass to `pdb2gmx` all at once. While this is supported, it requires you to carefully prepare the input file with appropriate chain identifiers or `TER` delimiters. I suspect you have not done this, hence why `pdb2gmx` is finding an internal residue when it should find a terminus, in the case of Leu141. ---
**Author:** ![kyrstyno](https://avatars.discourse-cdn.com/v4/letter/k/d07c76/32.png) [@kyrstyno](https://gromacs.bioexcel.eu/u/kyrstyno)\ **Post date:** [October 1, 2022, 5:34am 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/1164/28 "2022-10-01T05:34:37Z")
Thank you for pointing this out about the TER delimiters. I had to use editconf to create a pdb file from a .gro file, which is what I have available. Is there a better way to create a pdb file from a gro file to make sure that the chain identifiers are included? ---
**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 1, 2022, 10:37am 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/1164/29 "2022-10-01T10:37:09Z")
If you are starting with a `.gro` file, you simply have to add all the appropriate delimiters yourself, since `.gro` format does not support this information. ---
**Author:** ![ruhul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ruhul/32/2014_2.png) [@ruhul](https://gromacs.bioexcel.eu/u/ruhul)\ **Post date:** [February 28, 2023, 7:13pm 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/1164/30 "2023-02-28T19:13:07Z")
Hi, I am facing this error during creating a topology file for protein. Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2 Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 790) Fatal error: Atom OXT in residue SER 434 was not found in rtp entry SER with 11 atoms while sorting atoms. How can I solve it? Please help me. ---
**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 2, 2023, 2:57pm 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/1164/31 "2023-03-02T14:57:50Z")
Your problem is different than the one that started this thread, but in any case please provide the complete `pdb2gmx` terminal output, copied and pasted directly and including the command you gave. ---
**Author:** ![ruhul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ruhul/32/2014_2.png) [@ruhul](https://gromacs.bioexcel.eu/u/ruhul)\ **Post date:** [March 2, 2023, 4:17pm 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/1164/32 "2023-03-02T16:17:04Z")
ruhul@ruhul:~/MD/simulation$ gmx pdb2gmx -f protein\_processed.pdb -ignh -o protein\_processed.gro :-) GROMACS - gmx pdb2gmx, 2021.4-Ubuntu-2021.4-2 (-: ``` GROMACS is written by: Andrey Alekseenko Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Gilles Gouaillardet Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel ``` Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out [http://www.gromacs.org](http://www.gromacs.org) for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/ruhul/MD/simulation Command line: gmx pdb2gmx -f protein\_processed.pdb -ignh -o protein\_processed.gro Select the Force Field: From current directory: 1: CHARMM all-atom force field From ‘/usr/share/gromacs/top’: 2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) 10: GROMOS96 43a1 force field 11: GROMOS96 43a2 force field (improved alkane dihedrals) 12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9) 16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 1 Using the Charmm36-jul2022 force field in directory ./charmm36-jul2022.ff Opening force field file ./charmm36-jul2022.ff/watermodels.dat Select the Water Model: 1: TIP3P CHARMM-modified TIP3P water model (recommended over original TIP3P) 2: TIP3P\_ORIGINAL Original TIP3P water model 3: SPC SPC water model 4: SPCE SPC/E water model 5: TIP5P TIP5P water model 6: TIP4P TIP4P water model 7: TIP4PEW TIP4P/Ew water model 8: None 1 going to rename ./charmm36-jul2022.ff/aminoacids.r2b Opening force field file ./charmm36-jul2022.ff/aminoacids.r2b going to rename ./charmm36-jul2022.ff/carb.r2b Opening force field file ./charmm36-jul2022.ff/carb.r2b going to rename ./charmm36-jul2022.ff/cgenff.r2b Opening force field file ./charmm36-jul2022.ff/cgenff.r2b going to rename ./charmm36-jul2022.ff/ethers.r2b Opening force field file ./charmm36-jul2022.ff/ethers.r2b going to rename ./charmm36-jul2022.ff/lipid.r2b Opening force field file ./charmm36-jul2022.ff/lipid.r2b going to rename ./charmm36-jul2022.ff/metals.r2b Opening force field file ./charmm36-jul2022.ff/metals.r2b going to rename ./charmm36-jul2022.ff/na.r2b Opening force field file ./charmm36-jul2022.ff/na.r2b going to rename ./charmm36-jul2022.ff/silicates.r2b Opening force field file ./charmm36-jul2022.ff/silicates.r2b going to rename ./charmm36-jul2022.ff/solvent.r2b Opening force field file ./charmm36-jul2022.ff/solvent.r2b Reading protein\_processed.pdb… WARNING: all CONECT records are ignored Read 'D:\Megasync\Document\Research\Docking\RB Peptides\Docking\Antihypertensive\ACE\Final\MD simulation\ACE\_YY\_complex.pdbqt ', 4686 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 574 residues with 4686 atoms chain #res #atoms 1 ‘A’ 574 4686 All occupancies are one All occupancies are one Opening force field file ./charmm36-jul2022.ff/atomtypes.atp Reading residue database… (Charmm36-jul2022) Opening force field file ./charmm36-jul2022.ff/aminoacids.rtp Opening force field file ./charmm36-jul2022.ff/carb.rtp Opening force field file ./charmm36-jul2022.ff/cgenff.rtp Opening force field file ./charmm36-jul2022.ff/ethers.rtp Opening force field file ./charmm36-jul2022.ff/lipid.rtp Opening force field file ./charmm36-jul2022.ff/metals.rtp Opening force field file ./charmm36-jul2022.ff/na.rtp Opening force field file ./charmm36-jul2022.ff/silicates.rtp Opening force field file ./charmm36-jul2022.ff/solvent.rtp Opening force field file ./charmm36-jul2022.ff/aminoacids.hdb Opening force field file ./charmm36-jul2022.ff/carb.hdb Opening force field file ./charmm36-jul2022.ff/cgenff.hdb Opening force field file ./charmm36-jul2022.ff/ethers.hdb Opening force field file ./charmm36-jul2022.ff/lipid.hdb Opening force field file ./charmm36-jul2022.ff/metals.hdb Opening force field file ./charmm36-jul2022.ff/na.hdb Opening force field file ./charmm36-jul2022.ff/silicates.hdb Opening force field file ./charmm36-jul2022.ff/solvent.hdb Opening force field file ./charmm36-jul2022.ff/aminoacids.n.tdb Opening force field file ./charmm36-jul2022.ff/carb.n.tdb Opening force field file ./charmm36-jul2022.ff/cgenff.n.tdb Opening force field file ./charmm36-jul2022.ff/ethers.n.tdb Opening force field file ./charmm36-jul2022.ff/lipid.n.tdb Opening force field file ./charmm36-jul2022.ff/metals.n.tdb Opening force field file ./charmm36-jul2022.ff/na.n.tdb Opening force field file ./charmm36-jul2022.ff/silicates.n.tdb Opening force field file ./charmm36-jul2022.ff/solvent.n.tdb Opening force field file ./charmm36-jul2022.ff/aminoacids.c.tdb Opening force field file ./charmm36-jul2022.ff/carb.c.tdb Opening force field file ./charmm36-jul2022.ff/cgenff.c.tdb Opening force field file ./charmm36-jul2022.ff/ethers.c.tdb Opening force field file ./charmm36-jul2022.ff/lipid.c.tdb Opening force field file ./charmm36-jul2022.ff/metals.c.tdb Opening force field file ./charmm36-jul2022.ff/na.c.tdb Opening force field file ./charmm36-jul2022.ff/silicates.c.tdb Opening force field file ./charmm36-jul2022.ff/solvent.c.tdb Processing chain 1 ‘A’ (4686 atoms, 574 residues) Analysing hydrogen-bonding network for automated assignment of histidine protonation. 885 donors and 857 acceptors were found. There are 1153 hydrogen bonds Will use HISE for residue 91 Will use HISE for residue 153 Will use HISE for residue 248 Will use HISE for residue 256 Will use HISE for residue 258 Will use HISE for residue 263 Will use HISE for residue 273 Will use HISE for residue 353 Will use HISD for residue 382 Will use HISD for residue 383 Will use HISE for residue 387 Will use HISE for residue 410 Will use HISD for residue 426 Will use HISE for residue 428 Will use HISD for residue 442 Will use HISE for residue 513 Will use HISE for residue 534 Will use HISE for residue 543 Will use HISE for residue 548 Will use HISE for residue 610 Identified residue ASP40 as a starting terminus. Identified residue PRO617 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: MET86 HIS91 MET142 CYS152 HIS153 CYS158 MET169 SD391 NE2432 SD851 SG925 NE2935 SG966 SD1052 HIS91 NE2432 1.518 MET142 SD851 1.719 2.724 CYS152 SG925 3.387 4.410 2.180 HIS153 NE2935 4.077 4.941 2.704 0.887 CYS158 SG966 3.432 4.428 2.297 0.204 0.903 MET169 SD1052 3.816 4.467 2.275 1.597 1.158 1.681 MET223 SD1503 2.153 1.943 1.823 3.634 3.907 3.707 3.085 HIS248 NE21722 4.655 5.044 3.075 3.315 2.886 3.438 1.816 HIS256 NE21791 5.674 6.193 4.012 3.563 2.892 3.670 2.178 HIS258 NE21812 5.146 5.676 3.587 2.655 1.863 2.706 1.350 HIS263 NE21852 5.282 6.011 3.599 2.738 2.057 2.849 1.679 HIS273 NE21926 4.386 5.095 2.728 2.059 1.503 2.178 0.803 MET278 SD1961 3.393 4.083 1.835 1.489 1.314 1.595 0.441 MET299 SD2131 5.409 5.362 4.398 3.773 3.204 3.714 2.735 MET305 SD2175 4.285 4.291 3.385 2.964 2.612 2.903 2.123 MET315 SD2263 3.827 3.826 3.090 2.789 2.607 2.716 2.199 MET340 SD2469 2.565 2.853 2.220 2.232 2.551 2.155 2.420 CYS352 SG2562 2.750 3.244 1.936 1.663 1.901 1.611 1.741 HIS353 NE22572 2.537 2.840 1.516 2.255 2.401 2.292 1.693 CYS370 SG2716 2.784 3.189 2.069 1.851 2.064 1.788 1.885 HIS382 NE22807 3.937 3.612 3.302 3.550 3.377 3.514 2.680 HIS383 NE22817 2.920 2.808 2.155 3.001 3.028 3.023 2.192 MET385 SD2833 3.272 2.888 2.953 3.406 3.447 3.360 2.883 HIS387 NE22848 2.698 2.484 2.133 3.137 3.244 3.155 2.465 MET392 SD2895 3.187 2.433 3.260 4.055 4.196 4.014 3.618 HIS410 NE23038 2.576 2.013 2.408 3.691 3.876 3.709 3.115 HIS426 NE23152 4.579 4.203 3.889 3.986 3.695 3.945 2.995 HIS428 NE23170 5.658 5.412 4.778 4.394 3.884 4.336 3.324 HIS442 NE23248 5.906 5.804 4.750 4.389 3.754 4.377 3.033 MET448 SD3298 4.939 5.049 3.569 3.558 3.014 3.613 1.991 MET450 SD3315 4.465 4.340 3.390 3.584 3.196 3.600 2.238 CYS496 SG3720 4.415 5.063 2.722 2.726 2.348 2.876 1.462 HIS513 NE23852 2.506 2.771 1.422 2.504 2.644 2.567 1.818 HIS534 NE24037 4.613 4.197 3.780 4.326 4.030 4.342 3.052 CYS538 SG4065 4.744 4.210 4.022 4.638 4.367 4.649 3.405 HIS543 NE24098 5.303 4.802 4.488 4.941 4.575 4.950 3.618 HIS548 NE24134 5.357 5.090 4.301 4.516 4.042 4.535 3.077 CYS550 SG4149 4.861 4.332 4.135 4.664 4.370 4.667 3.435 MET566 SD4271 3.352 2.615 3.136 4.183 4.233 4.184 3.423 MET578 SD4370 3.923 3.320 3.367 4.642 4.583 4.695 3.543 MET587 SD4438 3.537 3.191 2.800 4.215 4.200 4.295 3.136 MET592 SD4468 4.154 4.006 3.061 3.866 3.618 3.935 2.496 HIS610 NE24630 6.092 6.339 4.558 4.278 3.582 4.353 2.737 MET223 HIS248 HIS256 HIS258 HIS263 HIS273 MET278 SD1503 NE21722 NE21791 NE21812 NE21852 NE21926 SD1961 HIS248 NE21722 3.196 HIS256 NE21791 4.427 1.309 HIS258 NE21812 4.145 1.774 1.315 HIS263 NE21852 4.422 1.769 1.043 1.069 HIS273 NE21926 3.566 1.477 1.523 1.059 0.926 MET278 SD1961 2.729 1.906 2.470 1.773 1.994 1.073 MET299 SD2131 4.201 3.242 3.367 2.429 3.490 3.125 2.987 MET305 SD2175 3.263 3.008 3.450 2.429 3.378 2.745 2.238 MET315 SD2263 2.989 3.252 3.807 2.779 3.645 2.916 2.216 MET340 SD2469 2.561 3.781 4.490 3.514 4.090 3.218 2.207 CYS352 SG2562 2.564 3.216 3.854 2.881 3.406 2.536 1.538 HIS353 NE22572 1.628 2.571 3.508 2.841 3.288 2.378 1.387 CYS370 SG2716 2.563 3.314 3.965 2.979 3.549 2.685 1.699 HIS382 NE22807 2.626 3.188 3.950 3.176 4.027 3.308 2.652 HIS383 NE22817 1.478 2.649 3.674 3.089 3.662 2.814 1.979 MET385 SD2833 2.292 3.632 4.485 3.666 4.423 3.604 2.745 HIS387 NE22848 1.295 2.947 3.998 3.415 3.968 3.103 2.218 MET392 SD2895 2.251 4.224 5.186 4.453 5.167 4.327 3.427 HIS410 NE23038 1.100 3.463 4.586 4.071 4.598 3.734 2.842 HIS426 NE23152 3.174 3.334 3.973 3.225 4.157 3.543 3.047 HIS428 NE23170 4.303 3.612 3.854 3.062 4.104 3.723 3.528 HIS442 NE23248 4.359 2.849 2.926 2.427 3.388 3.191 3.302 MET448 SD3298 3.333 1.330 1.839 1.665 2.346 2.014 2.189 MET450 SD3315 2.827 2.132 2.854 2.357 3.166 2.604 2.320 CYS496 SG3720 3.344 0.881 1.373 1.673 1.279 0.917 1.527 HIS513 NE23852 1.314 2.398 3.448 2.935 3.305 2.408 1.489 HIS534 NE24037 2.760 2.713 3.571 3.233 3.990 3.422 3.061 CYS538 SG4065 2.871 3.058 3.925 3.596 4.361 3.790 3.401 HIS543 NE24098 3.421 3.136 3.855 3.588 4.387 3.924 3.679 HIS548 NE24134 3.537 2.505 3.069 2.844 3.641 3.275 3.211 CYS550 SG4149 3.030 3.137 3.948 3.580 4.381 3.826 3.451 MET566 SD4271 1.770 3.612 4.682 4.166 4.821 4.020 3.235 MET578 SD4370 1.820 3.024 4.210 4.091 4.587 3.906 3.376 MET587 SD4438 1.396 2.555 3.822 3.790 4.139 3.441 2.923 MET592 SD4468 2.209 1.767 2.888 2.826 3.313 2.722 2.438 HIS610 NE24630 4.536 1.632 1.170 1.778 2.102 2.342 3.031 MET299 MET305 MET315 MET340 CYS352 HIS353 CYS370 SD2131 SD2175 SD2263 SD2469 SG2562 NE22572 SG2716 MET305 SD2175 1.145 MET315 SD2263 1.682 0.565 MET340 SD2469 3.130 1.999 1.474 CYS352 SG2562 2.898 1.807 1.411 0.695 HIS353 NE22572 2.977 1.938 1.660 1.367 1.065 CYS370 SG2716 2.825 1.713 1.276 0.544 0.204 1.099 HIS382 NE22807 1.838 1.069 0.996 2.041 2.077 1.800 1.943 HIS383 NE22817 2.744 1.789 1.567 1.730 1.637 0.794 1.584 MET385 SD2833 2.552 1.568 1.161 1.484 1.767 1.591 1.598 HIS387 NE22848 3.000 2.015 1.722 1.679 1.708 0.908 1.639 MET392 SD2895 3.274 2.375 1.980 1.975 2.404 2.125 2.238 HIS410 NE23038 3.520 2.570 2.246 2.048 2.237 1.496 2.151 HIS426 NE23152 1.475 1.164 1.339 2.613 2.614 2.379 2.485 HIS428 NE23170 0.738 1.527 1.983 3.452 3.330 3.292 3.228 HIS442 NE23248 1.151 1.987 2.529 3.927 3.621 3.395 3.577 MET448 SD3298 2.040 2.074 2.468 3.462 3.004 2.486 3.029 MET450 SD3315 1.653 1.405 1.722 2.826 2.550 2.021 2.508 CYS496 SG3720 3.604 3.234 3.402 3.671 3.035 2.557 3.177 HIS513 NE23852 3.187 2.212 1.988 1.748 1.470 0.417 1.512 HIS534 NE24037 2.207 2.005 2.206 3.217 3.098 2.439 3.023 CYS538 SG4065 2.411 2.238 2.406 3.396 3.342 2.687 3.252 HIS543 NE24098 2.301 2.415 2.694 3.836 3.735 3.138 3.650 HIS548 NE24134 1.909 2.172 2.569 3.783 3.537 2.987 3.488 CYS550 SG4149 2.269 2.161 2.355 3.414 3.363 2.764 3.268 MET566 SD4271 3.202 2.423 2.193 2.444 2.648 1.987 2.529 MET578 SD4370 3.583 3.052 3.023 3.433 3.403 2.455 3.349 MET587 SD4438 3.743 3.120 3.074 3.300 3.168 2.128 3.157 MET592 SD4468 2.802 2.410 2.559 3.222 2.937 2.043 2.934 HIS610 NE24630 2.888 3.255 3.709 4.697 4.154 3.723 4.213 HIS382 HIS383 MET385 HIS387 MET392 HIS410 HIS426 NE22807 NE22817 SD2833 NE22848 SD2895 NE23038 NE23152 HIS383 NE22817 1.251 MET385 SD2833 0.850 1.157 HIS387 NE22848 1.378 0.340 1.081 MET392 SD2895 1.499 1.622 0.832 1.395 HIS410 NE23038 1.751 0.985 1.304 0.671 1.169 HIS426 NE23152 0.643 1.824 1.434 1.979 1.971 2.312 HIS428 NE23170 1.803 2.891 2.569 3.109 3.162 3.524 1.241 HIS442 NE23248 2.331 3.054 3.165 3.344 3.805 3.826 1.887 MET448 SD3298 2.289 2.294 2.958 2.625 3.606 3.166 2.232 MET450 SD3315 1.269 1.577 2.002 1.873 2.613 2.363 1.228 CYS496 SG3720 3.559 2.886 3.869 3.162 4.497 3.715 3.800 HIS513 NE23852 1.960 0.779 1.799 0.884 2.238 1.403 2.519 HIS534 NE24037 1.364 1.757 2.039 1.944 2.390 2.194 1.232 CYS538 SG4065 1.485 1.958 2.109 2.094 2.346 2.242 1.306 HIS543 NE24098 1.859 2.459 2.584 2.631 2.874 2.827 1.496 HIS548 NE24134 1.974 2.460 2.776 2.718 3.257 3.080 1.637 CYS550 SG4149 1.446 2.047 2.116 2.191 2.380 2.361 1.184 MET566 SD4271 1.406 1.258 1.197 1.086 0.973 0.798 1.820 MET578 SD4370 2.191 1.767 2.369 1.766 2.340 1.634 2.410 MET587 SD4438 2.424 1.628 2.540 1.660 2.622 1.644 2.745 MET592 SD4468 1.990 1.574 2.452 1.811 2.843 2.145 2.141 HIS610 NE24630 3.636 3.642 4.327 3.974 4.989 4.512 3.488 HIS428 HIS442 MET448 MET450 CYS496 HIS513 HIS534 NE23170 NE23248 SD3298 SD3315 SG3720 NE23852 NE24037 HIS442 NE23248 1.163 MET448 SD3298 2.321 1.545 MET450 SD3315 1.745 1.532 1.064 CYS496 SG3720 4.093 3.428 1.988 2.694 HIS513 NE23852 3.464 3.475 2.437 2.030 2.432 HIS534 NE24037 1.990 1.953 1.752 0.899 3.372 2.372 CYS538 SG4065 2.091 2.161 2.105 1.255 3.729 2.617 0.371 HIS543 NE24098 1.899 1.824 2.055 1.386 3.868 3.081 0.711 HIS548 NE24134 1.724 1.197 1.312 0.994 3.244 2.944 0.958 CYS550 SG4149 1.911 2.031 2.115 1.247 3.804 2.721 0.439 MET566 SD4271 3.053 3.440 3.049 2.105 4.014 1.934 1.698 MET578 SD4370 3.426 3.378 2.674 2.054 3.609 2.197 1.478 MET587 SD4438 3.728 3.550 2.529 2.126 3.053 1.784 1.847 MET592 SD4468 2.850 2.468 1.394 1.154 2.434 1.818 1.176 HIS610 NE24630 3.204 2.111 1.384 2.411 2.198 3.656 2.984 CYS538 HIS543 HIS548 CYS550 MET566 MET578 MET587 SG4065 NE24098 NE24134 SG4149 SD4271 SD4370 SD4438 HIS543 NE24098 0.593 HIS548 NE24134 1.160 0.835 CYS550 SG4149 0.203 0.497 1.100 MET566 SD4271 1.642 2.227 2.643 1.743 MET578 SD4370 1.443 1.925 2.278 1.643 1.368 MET587 SD4438 1.947 2.399 2.519 2.141 1.727 0.754 MET592 SD4468 1.453 1.724 1.520 1.594 2.044 1.332 1.156 HIS610 NE24630 3.294 3.074 2.260 3.289 4.408 3.845 3.645 MET592 SD4468 HIS610 NE24630 2.564 Linking CYS-152 SG-925 and CYS-158 SG-966… Linking CYS-352 SG-2562 and CYS-370 SG-2716… Linking CYS-538 SG-4065 and CYS-550 SG-4149… Start terminus ASP-40: NH3+ End terminus PRO-617: COO- Opening force field file ./charmm36-jul2022.ff/aminoacids.arn * * * Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2 Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 790) Fatal error: Atom OXT in residue SER 434 was not found in rtp entry SER with 11 atoms while sorting atoms. . For more information and tips for troubleshooting, please check the GROMACS website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors) ---
**Author:** ![ruhul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ruhul/32/2014_2.png) [@ruhul](https://gromacs.bioexcel.eu/u/ruhul)\ **Post date:** [March 2, 2023, 4:20pm 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/1164/33 "2023-03-02T16:20:50Z")
[Protein.dat](https://gromacs.bioexcel.eu/uploads/short-url/7ffsUIRCOJqeY0Ejc6ZgQiHvbI7.dat) (850.2 KB) ---
**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 2, 2023, 6:49pm 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/1164/34 "2023-03-02T18:49:36Z")
You have a gap in the chain, meaning there are missing residues and false termini in residues 434 and 439: ```auto ATOM 3907 N SER A 434 64.099 23.522 31.944 1.00 0.00 N ATOM 3908 CA SER A 434 65.416 23.262 31.311 1.00 0.00 C ATOM 3909 C SER A 434 65.679 24.163 30.097 1.00 0.00 C ATOM 3910 O SER A 434 66.214 25.277 30.281 1.00 0.00 O ATOM 3911 CB SER A 434 65.534 21.781 30.934 1.00 0.00 C ATOM 3912 OG SER A 434 64.417 21.381 30.127 1.00 0.00 O ATOM 3913 H SER A 434 63.313 23.210 31.412 1.00 0.00 H ATOM 3914 HG SER A 434 64.567 20.451 29.786 1.00 0.00 H ATOM 3915 OXT SER A 434 65.204 23.790 29.011 1.00 0.00 O ATOM 3916 N SER A 439 64.493 32.707 21.995 1.00 0.00 N ATOM 3917 CA SER A 439 63.945 31.893 20.883 1.00 0.00 C ATOM 3918 C SER A 439 62.467 32.226 20.609 1.00 0.00 C ATOM 3919 O SER A 439 61.613 32.125 21.492 1.00 0.00 O ATOM 3920 CB SER A 439 64.090 30.389 21.178 1.00 0.00 C ATOM 3921 OG SER A 439 63.479 29.572 20.164 1.00 0.00 O ATOM 3922 H1 SER A 439 63.787 33.327 22.340 1.00 0.00 H ATOM 3923 HG SER A 439 63.812 28.626 20.264 1.00 0.00 H ATOM 3924 H2 SER A 439 64.827 32.143 22.737 1.00 0.00 H ATOM 3925 H3 SER A 439 65.278 33.229 21.696 1.00 0.00 H ``` `pdb2gmx` is finding OXT (which corresponds to a C-terminal acidic oxygen) in a non-terminal residue, so it triggers an error. Then the presence of H[123] in residue 439 means that is a new N-terminus, but there is a gap from residues 435-438 that means you have an incomplete structure. ---
**Author:** ![ruhul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ruhul/32/2014_2.png) [@ruhul](https://gromacs.bioexcel.eu/u/ruhul)\ **Post date:** [March 2, 2023, 7:35pm 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/1164/35 "2023-03-02T19:35:20Z")
By default, this protein (PDB ID:1o86) structure has to miss these residues (435 - 438). Please check the raw file of that protein which I have attached here. You can also check the structure from this link ([RCSB PDB - 1O86: Crystal Structure of Human Angiotensin Converting Enzyme in complex with lisinopril.](https://www.rcsb.org/structure/1O86)). I don’t understand what should I do. [protein(PDB:1o86).dat](https://gromacs.bioexcel.eu/uploads/short-url/wbh5xDt6ZKSJqKioljIMUDElo3d.dat) (460.7 KB) ---
**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 2, 2023, 8:22pm 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/1164/36 "2023-03-02T20:22:38Z")
You can’t simulate something reasonably with gaps in the chains. You need to model in the missing residues with software like Modeller or Rosetta. ---
**Author:** ![ruhul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ruhul/32/2014_2.png) [@ruhul](https://gromacs.bioexcel.eu/u/ruhul)\ **Post date:** [March 3, 2023, 6:12am 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/1164/37 "2023-03-03T06:12:25Z")
Ok sir. Thank you for your kind information. But there is one more thing if I replace the OXT with O in residue SER 434, then it creates the topology file without any fatal error. So what’s your opinion about this? Is this the right way to solve the 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 3, 2023, 1:42pm 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/1164/38 "2023-03-03T13:42:02Z")
You will have an artificially strained bond that will never minimize properly, and you will still be missing the residues that should be in between 434 and 439. The outcomes of the simulations will be fictitious. Build in the missing residues. ---
**Author:** ![ruhul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ruhul/32/2014_2.png) [@ruhul](https://gromacs.bioexcel.eu/u/ruhul)\ **Post date:** [March 3, 2023, 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/1164/39 "2023-03-03T14:09:41Z")
Ok sir. I have another question. I want to perform MD simulation after molecular docking(protein-peptide docking). I already performed docking with this protein(1o86) without building missing residues. After building missing residues, should I again perform docking? Then docked complex will use for MD simulation? ---
**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 3, 2023, 2:23pm 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/1164/40 "2023-03-03T14:23:19Z")
If the missing residues might affect the docked pose, they need to be there before you try to dock anything to it. If they are far away, building them after docking is probably fine. [Previous 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=1) [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=3)