# Atom OP3 in residue DA 1 was not found in rtp entry DA5 with 30 atoms while sorting atoms **URL:** \ **Category:** User discussions\ **Tags:** pdb2gmx, forcefield, mdrun\ **Created:** [July 4, 2024, 10:26am UTC](https://gromacs.bioexcel.eu/t/atom-op3-in-residue-da-1-was-not-found-in-rtp-entry-da5-with-30-atoms-while-sorting-atoms/9570 "2024-07-04T10:26:50Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![intomybioverse](https://avatars.discourse-cdn.com/v4/letter/i/67e7ee/32.png) [@intomybioverse](https://gromacs.bioexcel.eu/u/intomybioverse)\ **Post date:** [July 4, 2024, 10:26am UTC](https://gromacs.bioexcel.eu/t/atom-op3-in-residue-da-1-was-not-found-in-rtp-entry-da5-with-30-atoms-while-sorting-atoms/9570/1 "2024-07-04T10:26:51Z")
I have converted a .cif file into .pdb file (myfile.txt, attached here) using openbabel commandline: obabel -i cif myfile.cif -o pdb -O myfile.pdb [myfile.txt](https://gromacs.bioexcel.eu/uploads/short-url/9kDnHBYNFyNHWeZoP1PKtHK05AN.txt) (171.6 KB) But after this, pdb2gmx conversion in gromacs is not running. I want to use AMBER99SB protein, nucleic AMBER94 or AMBER99SB-ILDN protein, nucleic AMBER94. Please help! Error: $ gmx pdb2gmx -f start\_clean.pdb -o complex.gro -ignh :-) 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: /media/soumya/HD1/ParamShakti/SCR/AF3\_july1/3m-dna Command line: gmx pdb2gmx -f start\_clean.pdb -o complex.gro -ignh Select the Force Field: From ‘/usr/share/gromacs/top’: 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) 9: GROMOS96 43a1 force field 10: GROMOS96 43a2 force field (improved alkane dihedrals) 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9) 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 6 Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat Select the Water Model: 1: TIP3P TIP 3-point, recommended 2: TIP4P TIP 4-point 3: TIP4P-Ew TIP 4-point optimized with Ewald 4: TIP5P TIP 5-point (see [OPLS/AA not compatible with TIP5P - Redmine #1348 (#1348) · Issues · GROMACS / GROMACS · GitLab](https://gitlab.com/gromacs/gromacs/-/issues/1348) for issues) 5: SPC simple point charge 6: SPC/E extended simple point charge 7: None 1 going to rename amber99sb-ildn.ff/aminoacids.r2b Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b going to rename amber99sb-ildn.ff/dna.r2b Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b going to rename amber99sb-ildn.ff/rna.r2b Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b Reading start\_clean.pdb… WARNING: all CONECT records are ignored Read '5fbbe3dda33eebc1 ', 1142 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 3 chains and 0 blocks of water and 89 residues with 1142 atoms chain #res #atoms 1 ‘A’ 61 566 2 ‘B’ 14 291 3 ‘C’ 14 285 All occupancies are one All occupancies are one Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp Reading residue database… (Amber99sb-ildn) Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.1# Processing chain 1 ‘A’ (566 atoms, 61 residues) Analysing hydrogen-bonding network for automated assignment of histidine protonation. 126 donors and 93 acceptors were found. There are 118 hydrogen bonds Will use HISE for residue 21 Will use HISD for residue 60 Identified residue THR1 as a starting terminus. Identified residue LYS61 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HIS21 MET54 NE2191 SD495 MET54 SD495 2.081 HIS60 NE2556 1.197 1.389 Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn Checking for duplicate atoms… Generating any missing hydrogen atoms and/or adding termini. Now there are 61 residues with 1147 atoms Chain time… Back Off! I just backed up topol\_Protein\_chain\_A.itp to ./#topol\_Protein\_chain\_A.itp.1# Making bonds… Number of bonds was 1159, now 1158 Generating angles, dihedrals and pairs… Before cleaning: 3023 pairs Before cleaning: 3076 dihedrals Keeping all generated dihedrals Making cmap torsions… There are 3076 dihedrals, 247 impropers, 2074 angles 2999 pairs, 1158 bonds and 0 virtual sites Total mass 8010.418 a.m.u. Total charge 11.000 e Writing topology Back Off! I just backed up posre\_Protein\_chain\_A.itp to ./#posre\_Protein\_chain\_A.itp.1# Processing chain 2 ‘B’ (291 atoms, 14 residues) Identified residue DA1 as a starting terminus. Identified residue DG14 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn Opening force field file /usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn * * * Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2 Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 790) Fatal error: Atom OP3 in residue DA 1 was not found in rtp entry DA5 with 30 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:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [July 5, 2024, 6:24am UTC](https://gromacs.bioexcel.eu/t/atom-op3-in-residue-da-1-was-not-found-in-rtp-entry-da5-with-30-atoms-while-sorting-atoms/9570/2 "2024-07-05T06:24:49Z")
It’s saying the AMBER forcefield does not include OP3 in the 5’ terminal A nucleotide, try removing it from the pdb file ---
**Author:** ![intomybioverse](https://avatars.discourse-cdn.com/v4/letter/i/67e7ee/32.png) [@intomybioverse](https://gromacs.bioexcel.eu/u/intomybioverse)\ **Post date:** [July 5, 2024, 10:09am UTC](https://gromacs.bioexcel.eu/t/atom-op3-in-residue-da-1-was-not-found-in-rtp-entry-da5-with-30-atoms-while-sorting-atoms/9570/3 "2024-07-05T10:09:31Z")
Thank you so much! It’s working now.