[gmx-users] (no subject)

[Justin Lemkul]

On 2/14/20 12:05 AM, Neha Tiwari wrote:
> Dear Gromacs experts,
> I have generated topology files(.itp) of the ligand from the ATB server and
> everything goes well, but when it comes to generating ions.tpr file, I am
> getting following error.
>
>
> $ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
>
>                        :-) GROMACS - gmx grompp, 2018.1 (-:
>
>
>
>                              GROMACS is written by:
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>       Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C.
> Berendsen
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>
>    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
>
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> 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.
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>
>
> 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 grompp, version 2018.1
>
> Executable:   /usr/bin/gmx
>
> Data prefix:  /usr
>
> Working dir:  /home/ya/Desktop/Neha/fecA/gromos
>
> Command line:
>
>    gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
>
>
>
> Ignoring obsolete mdp entry 'title'
>
>
>
> NOTE 1 [file ions.mdp]:
>
>    With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
>
>    that with the Verlet scheme, nstlist has no effect on the accuracy of
>
>    your simulation.
>
>
>
> Setting the LD random seed to 49113858
>
> Generated 165 of the 1596 non-bonded parameter combinations
>
> Excluding 3 bonded neighbours molecule type 'Protein'
>
> Excluding 3 bonded neighbours molecule type '4JCP'
>
> Excluding 2 bonded neighbours molecule type 'SOL'
>
>
>
> NOTE 2 [file topol.top, line 45350]:
>
>    System has non-zero total charge: -14.000000
>
>    Total charge should normally be an integer. See
>
>    http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>
>    for discussion on how close it should be to an integer.
>
>
>
>
>
>
>
> Removing all charge groups because cutoff-scheme=Verlet
>
>
>
> ERROR 1 [file topol.top, line 45350]:
>
>    atom O10 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)
>
>
>
>
>
>
>
> ERROR 2 [file topol.top, line 45350]:
>
>    atom C2 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)
>
>
>
>
>
>
>
> ERROR 3 [file topol.top, line 45350]:
>
>    atom O9 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)
>
>
>
>
>
>
>
> ERROR 4 [file topol.top, line 45350]:
>
>    atom Fe14 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)
>
>
>
>
>
>
>
> ERROR 5 [file topol.top, line 45350]:
>
>    atom C3 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)
>
>
>
>
>
>
>
> ERROR 6 [file topol.top, line 45350]:
>
>    atom C4 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)
>
>
>
>
>
>
>
> ERROR 7 [file topol.top, line 45350]:
>
>    atom O11 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)
>
>
>
>
>
>
>
> ERROR 8 [file topol.top, line 45350]:
>
>    atom H19 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)
>
>
>
>
>
>
>
> ERROR 9 [file topol.top, line 45350]:
>
>    atom C6 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)
>
>
>
>
>
>
>
> ERROR 10 [file topol.top, line 45350]:
>
>    atom O12 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)
>
>
>
>
>
>
>
> ERROR 11 [file topol.top, line 45350]:
>
>    atom O13 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)
>
>
>
>
>
>
>
> ERROR 12 [file topol.top, line 45350]:
>
>    atom C5 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)
>
>
>
>
>
>
>
> ERROR 13 [file topol.top, line 45350]:
>
>    atom C1 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)
>
>
>
>
>
>
>
> ERROR 14 [file topol.top, line 45350]:
>
>    atom O7 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)
>
>
>
>
>
>
>
> ERROR 15 [file topol.top, line 45350]:
>
>    atom O8 (Res 4JCP-1) has mass 0 (state A) / 0 (state B)
>
>
>
>
>
>
>
> There were 2 notes
>
>
>
> -------------------------------------------------------
>
> Program:     gmx grompp, version 2018.1
>
> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2137)
>
>
>
> Fatal error:
>
> There were 15 errors in input file(s)
>

Likely the format/contents of those topology lines are wrong if grompp 
finds zero mass.

-Justin

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Justin A. Lemkul, Ph.D.
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