# Why did I get an error related to the terminal caps? **URL:** \ **Category:** User discussions\ **Tags:** pdb2gmx, forcefield\ **Created:** [December 13, 2021, 12:28am UTC](https://gromacs.bioexcel.eu/t/why-did-i-get-an-error-related-to-the-terminal-caps/3291 "2021-12-13T00:28:45Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![Natsulait](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/natsulait/32/1045_2.png) [@Natsulait](https://gromacs.bioexcel.eu/u/Natsulait)\ **Post date:** [December 13, 2021, 12:28am UTC](https://gromacs.bioexcel.eu/t/why-did-i-get-an-error-related-to-the-terminal-caps/3291/1 "2021-12-13T00:28:45Z")
GROMACS version: gmx pdb2gmx, version 2021.3 GROMACS modification: No Purpose: To cap both termini of a protein by ACE and NME and make the topology file. My attempt: 1. To add ACE and NME by PyMOL and NME is renamed to CT1. 2. `gmx pdb2gmx -ff charmm27 -f protein_test.pdb -water tip3p` I tried to make the topology file via `gmx pdb2gmx` command, but I failed and got the following error. Could you please help me to resolve this issue? ```auto $ bash test.sh :-) GROMACS - gmx pdb2gmx, 2021.3 (-: 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 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 2021.3 Executable: /Users/me/.local/gromacs-2021.3/build/bin/gmx Data prefix: /Users/me/.local/gromacs-2021.3 (source tree) Working dir: /Users/me/Dropbox/00_Research/16_koff_estimation/data/02_prep_system/thrombin/1bmn/test Command line: gmx pdb2gmx -f protein_test.pdb -ff charmm27 -water tip3p Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/rna.r2b Reading protein_test.pdb... Read '', 91 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 11 residues with 91 atoms chain #res #atoms 1 'I' 11 91 All occupancies are one All occupancies are one Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/atomtypes.atp Reading residue database... (Charmm27) Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/aminoacids.rtp Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/dna.rtp Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/lipids.rtp Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/rna.rtp Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/aminoacids.hdb Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/dna.hdb Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/lipids.hdb Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/rna.hdb Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/aminoacids.n.tdb Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/dna.n.tdb Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/rna.n.tdb Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/aminoacids.c.tdb Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/dna.c.tdb Opening force field file /Users/me/.local/gromacs-2021.3/share/top/charmm27.ff/rna.c.tdb Processing chain 1 'I' (91 atoms, 11 residues) Identified residue ACE55 as a starting terminus. Identified residue CT364 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Start terminus ACE-55: NH3+ End terminus CT3-64: CT3 ------------------------------------------------------- Program: gmx pdb2gmx, version 2021.3 Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1104) Fatal error: atom N not found in buiding block 1ACE while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- ``` ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [December 13, 2021, 7:51am UTC](https://gromacs.bioexcel.eu/t/why-did-i-get-an-error-related-to-the-terminal-caps/3291/2 "2021-12-13T07:51:38Z")
What are you trying to build? The error says There is a mismatching or missing atoms from your input pdb with that of files in ff. Also, did you tried with -ter flag? ---
**Author:** ![ebriand](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ebriand/32/2314_2.png) [@ebriand](https://gromacs.bioexcel.eu/u/ebriand)\ **Post date:** [December 13, 2021, 7:57am UTC](https://gromacs.bioexcel.eu/t/why-did-i-get-an-error-related-to-the-terminal-caps/3291/3 "2021-12-13T07:57:43Z")
ACE and NME cap require an empty terminus (“None”). The default behavior of pdb2gmx is to try to add NH3+ and COO- terminus as for a normal peptide. As suggested, use the `-ter` command line flag and select None for terminus at both end. ---
**Author:** ![Natsulait](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/natsulait/32/1045_2.png) [@Natsulait](https://gromacs.bioexcel.eu/u/Natsulait)\ **Post date:** [December 13, 2021, 9:26am UTC](https://gromacs.bioexcel.eu/t/why-did-i-get-an-error-related-to-the-terminal-caps/3291/4 "2021-12-13T09:26:32Z")
> ACE and NME cap require an empty terminus (“None”). The default behavior of pdb2gmx is to try to add NH3+ and COO- terminus as for a normal peptide. As suggested, use the `-ter` command line flag and select None for terminus at both end. Thank you. I have resolved the issue. I did not know how `-ter None` works. After using `-ter` flag and selecting `None`, I succeed in getting a structure whose termini are capped by aceyl and nmetyl groups :)