[gmx-users] Fatal error: Atom O4 in residue GLU 7 was not found in rtp entry
Navneet Kumar Singh
navneetcdl at gmail.com
Fri Sep 6 17:49:10 CEST 2019
Yeah!
But I don't want any charge at terminal residues. I think I should cap
these by acetyl or amide moiety. Let me try this.
On Fri, 6 Sep 2019, 19:45 Justin Lemkul, <jalemkul at vt.edu> wrote:
>
>
> 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
>
> ==================================================
>
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