[gmx-users] Fatal error: Atom O4 in residue GLU 7 was not found in rtp entry

Fri Sep 6 16:14:59 CEST 2019

On 9/6/19 4:32 AM, Navneet Kumar Singh wrote:
> Hello Everyone!
>
> I am trying to simulate five peptides along with water using GROMACS.
> I have used the PACKMOL to prepare initail PDB files.
> Peptide were made using Schrodinger Maestro.
> I have got a final PDB file having the water molecules and randowmly
> distributed peptides.
>
>
> After that I am using command pdb2gmx using the CHARMM36 force field.
>
> Following are the commands and its output,
>
> -------------------------------------------------------------------------------------------------------------
> gmx pdb2gmx -f final.pdb -o final.gro -water spce -ignh -ter
>                       :-) GROMACS - gmx pdb2gmx, 2018.4 (-:
>
>                              GROMACS is written by:
>       Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C.
> Berendsen
>      Par Bjelkmar    Aldert van Buuren   Rudi van Drunen     Anton Feenstra
>    Gerrit Groenhof    Aleksei Iupinov   Christoph Junghans   Anca Hamuraru
>   Vincent Hindriksen Dimitrios Karkoulis    Peter Kasson        Jiri Kraus
>
>    Carsten Kutzner      Per Larsson      Justin A. Lemkul    Viveca Lindahl
>    Magnus Lundborg   Pieter Meulenhoff    Erik Marklund      Teemu Murtola
>      Szilard Pall       Sander Pronk      Roland Schulz     Alexey Shvetsov
>     Michael Shirts     Alfons Sijbers     Peter Tieleman    Teemu Virolainen
>   Christian Wennberg    Maarten Wolf
>                             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) 2001-2017, 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 2018.4
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Working dir:  /home/navneet/Desktop/amyloid
> Command line:
>    gmx pdb2gmx -f final.pdb -o final.gro -water spce -ignh -ter
>
>
> Select the Force Field:
>  From current directory:
>   1: CHARMM36 all-atom force field (March 2019)
>  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: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI:
> 10.1007/s00249-011-0700-9)
> 17: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI:
> 10.1007/s00249-011-0700-9)
> 18: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 1
>
> Using the Charmm36-mar2019 force field in directory ./charmm36-mar2019.ff
>
> Opening force field file ./charmm36-mar2019.ff/merged.r2b
> Reading final.pdb...
> Read 'Built with Packmol through Packmol Memgen', 5305 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 1 chains and 1 blocks of water and 5035 residues with 5305 atoms
>
>    chain  #res #atoms
>    1 'A'    35    305
>    2 ' '  5000   5000  (only water)
>
>
> WARNING: there were 5000 atoms with zero occupancy and 0 atoms with
>           occupancy unequal to one (out of 5305 atoms). Check your pdb file.
>
> Opening force field file ./charmm36-mar2019.ff/atomtypes.atp
> Atomtype 447
> Reading residue database... (charmm36-mar2019)
> Opening force field file ./charmm36-mar2019.ff/merged.rtp
> Residue 1318
> Sorting it all out...
> Opening force field file ./charmm36-mar2019.ff/merged.hdb
> Opening force field file ./charmm36-mar2019.ff/merged.n.tdb
> Opening force field file ./charmm36-mar2019.ff/merged.c.tdb
>
> Back Off! I just backed up topol.top to ./#topol.top.2#
> Processing chain 1 'A' (305 atoms, 35 residues)
> Identified residue LYS1 as a starting terminus.
> Identified residue GLU7 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Select start terminus type for LYS-1
>   0: NH3+
>   1: NH2
>   2: 5TER
>   3: None
> 1
> Start terminus LYS-1: NH2
> Select end terminus type for GLU-7
>   0: COO-
>   1: COOH
>   2: CT2
>   3: 3TER
>   4: None
> 1
> End terminus GLU-7: COOH

These are curious choices; there is no pH value at which both termini 
will be in their neutral forms. You may wish to reconsider what 
chemistry you're assigning.

> Opening force field file ./charmm36-mar2019.ff/merged.arn
>
> -------------------------------------------------------
> Program:     gmx pdb2gmx, version 2018.4
> Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 753)
>
> Fatal error:
> Atom O4 in residue GLU 7 was not found in rtp entry GLU with 15 atoms
> while sorting atoms.
> .

Check your input coordinate file because apparently the atom names do 
not use standard nomenclature.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================