# Pdb2gmx - "This chain does not appear to contain a recognized chain molecule." but ion is in the FF **URL:** \ **Category:** User discussions\ **Tags:** mdrun\ **Created:** [September 14, 2021, 1:08am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-this-chain-does-not-appear-to-contain-a-recognized-chain-molecule-but-ion-is-in-the-ff/2810 "2021-09-14T01:08:37Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![csandall](https://avatars.discourse-cdn.com/v4/letter/c/a88e4f/32.png) [@csandall](https://gromacs.bioexcel.eu/u/csandall)\ **Post date:** [September 14, 2021, 1:08am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-this-chain-does-not-appear-to-contain-a-recognized-chain-molecule-but-ion-is-in-the-ff/2810/1 "2021-09-14T01:08:37Z")
GROMACS version: 2020.4 GROMACS modification: No **I’m hoping for some help running pdb2gmx on a protein which is bound to ADP and Mg2+.** **I have ADP and MG on different chains, and both are in the charmm36-feb2021 forcefield .rtp, but I keep getting the following error:** > Writing topology > > Processing chain 3 ‘I’ (1 atoms, 1 residues) > > Residue MG1038 has type ‘Ion’, assuming it is not linked into a chain. > > Problem with chain definition, or missing terminal residues. > > This chain does not appear to contain a recognized chain molecule. > > If this is incorrect, you can edit residuetypes.dat to modify the behavior. **I have included the entire output below for reference. If anyone can help I would really appreciate it! Thanks.** * * * > Last login: Mon Sep 13 18:39:44 on ttys000 > gmx pdb2gmx -f sm1\_ADPMg\_start.pdb -o sm1\_ADPMg\_start\_processed.gro > :-) GROMACS - gmx pdb2gmx, 2020.4 (-: > > ``` > GROMACS is written by: > 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 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 2020.4 > Executable: /usr/local/gromacs/bin/gmx > Data prefix: /usr/local/gromacs > Working dir: … > Command line: > gmx pdb2gmx -f sm1\_ADPMg\_start.pdb -o sm1\_ADPMg\_start\_processed.gro > > Select the Force Field: > From current directory: > 1: CHARMM36 all-atom force field (July 2020) > From ‘/usr/local/gromacs/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-feb2021 force field in directory ./charmm36-feb2021.ff > > Opening force field file ./charmm36-feb2021.ff/watermodels.dat > > Select the Water Model: > 1: TIP3P TIP 3-point, recommended, by default uses CHARMM TIP3 with LJ on H > 2: TIP4P TIP 4-point > 3: TIP5P TIP 5-point > 4: SPC simple point charge > 5: SPC/E extended simple point charge > 6: None > 1 > going to rename ./charmm36-feb2021.ff/merged.r2b > Opening force field file ./charmm36-feb2021.ff/merged.r2b > Reading sm1\_ADPMg\_start.pdb… > Read ‘’, 14436 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 904 residues with 14436 atoms > > chain #res #atoms > 1 ‘P’ 902 14396 > 2 ‘H’ 1 39 > 3 ‘I’ 1 1 > > All occupancies are one > Opening force field file ./charmm36-feb2021.ff/atomtypes.atp > Reading residue database… (Charmm36-feb2021) > Opening force field file ./charmm36-feb2021.ff/merged.rtp > Opening force field file ./charmm36-feb2021.ff/merged.hdb > Opening force field file ./charmm36-feb2021.ff/merged.n.tdb > Opening force field file ./charmm36-feb2021.ff/merged.c.tdb > Processing chain 1 ‘P’ (14396 atoms, 902 residues) > Identified residue ASP135 as a starting terminus. > Identified residue TRP1036 as a ending terminus. > 8 out of 8 lines of specbond.dat converted successfully > Special Atom Distance matrix: ( **DID NOT INCLUDE TO SAVE SPACE** ) > Start terminus ASP-135: NH3+ > End terminus TRP-1036: COO- > Opening force field file ./charmm36-feb2021.ff/merged.arn > Checking for duplicate atoms… > Generating any missing hydrogen atoms and/or adding termini. > Now there are 902 residues with 14397 atoms > Chain time… > Making bonds… > Number of bonds was 14534, now 14534 > Generating angles, dihedrals and pairs… > Before cleaning: 38175 pairs > Before cleaning: 38495 dihedrals > Keeping all generated dihedrals > Making cmap torsions… > There are 900 cmap torsion pairs > There are 38495 dihedrals, 2510 impropers, 26286 angles > 37953 pairs, 14534 bonds and 0 virtual sites > Total mass 102555.718 a.m.u. > Total charge -8.000 e > Writing topology > Processing chain 2 ‘H’ (39 atoms, 1 residues) > Problem with chain definition, or missing terminal residues. > This chain does not appear to contain a recognized chain molecule. > If this is incorrect, you can edit residuetypes.dat to modify the behavior. > 8 out of 8 lines of specbond.dat converted successfully > Opening force field file ./charmm36-feb2021.ff/merged.arn > Checking for duplicate atoms… > Generating any missing hydrogen atoms and/or adding termini. > Now there are 1 residues with 39 atoms > Chain time… > Making bonds… > Number of bonds was 41, now 41 > Generating angles, dihedrals and pairs… > Before cleaning: 88 pairs > Before cleaning: 98 dihedrals > Keeping all generated dihedrals > Making cmap torsions… > There are 98 dihedrals, 2 impropers, 71 angles > 85 pairs, 41 bonds and 0 virtual sites > Total mass 424.183 a.m.u. > Total charge -3.000 e > Writing topology > Processing chain 3 ‘I’ (1 atoms, 1 residues) > Residue MG1038 has type ‘Ion’, assuming it is not linked into a chain. > Problem with chain definition, or missing terminal residues. > This chain does not appear to contain a recognized chain molecule. > If this is incorrect, you can edit residuetypes.dat to modify the behavior. > 8 out of 8 lines of specbond.dat converted successfully > Opening force field file ./charmm36-feb2021.ff/merged.arn > Checking for duplicate atoms… > Generating any missing hydrogen atoms and/or adding termini. > Now there are 1 residues with 1 atoms > Chain time… > Making bonds… > No bonds > Generating angles, dihedrals and pairs… > Making cmap torsions… > There are 0 dihedrals, 0 impropers, 0 angles > 0 pairs, 0 bonds and 0 virtual sites > Total mass 24.305 a.m.u. > Total charge 2.000 e > Writing topology > Including chain 1 in system: 14397 atoms 902 residues > Including chain 2 in system: 39 atoms 1 residues > Including chain 3 in system: 1 atoms 1 residues > Now there are 14437 atoms and 904 residues > Total mass in system 103004.206 a.m.u. > Total charge in system -9.000 e > > Writing coordinate file… > --------- PLEASE NOTE ------------ > You have successfully generated a topology from: sm1\_ADPMg\_start.pdb. > The Charmm36-feb2021 force field and the tip3p water model are used. > --------- ETON ESAELP ------------ > > GROMACS reminds you: “They don’t have any beavers in India, so they have to simulate them” (The Tubes) ---
**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 14, 2021, 1:31am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-this-chain-does-not-appear-to-contain-a-recognized-chain-molecule-but-ion-is-in-the-ff/2810/2 "2021-09-14T01:31:45Z")
There is no problem here. The program completed successfully. It’s just a verbose message that can help in debugging if you had some kind of modified/custom residue that should be part of a chain but isn’t. ---
**Author:** ![csandall](https://avatars.discourse-cdn.com/v4/letter/c/a88e4f/32.png) [@csandall](https://gromacs.bioexcel.eu/u/csandall)\ **Post date:** [September 14, 2021, 1:32am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-this-chain-does-not-appear-to-contain-a-recognized-chain-molecule-but-ion-is-in-the-ff/2810/3 "2021-09-14T01:32:30Z")
Thanks very much!