[gmx-users] Can you help regarding this

[Dallas Warren]

What specifically do you need help with? Both the error messages there are
explicit about what the issues are, first you have failed to correctly
adjust the number of molecules of the topology (.top) to match the
coordinate file. You also have a +10 net charge, which is unlikely to be a
good idea.

On Sat, 14 Mar. 2020, 4:58 pm Kushal Roy, <kushalrajroyfc at gmail.com> wrote:

>                             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 grompp, version 2018.1
> Executable:   /usr/bin/gmx
> Data prefix:  /usr
> Working dir:  /mnt/c/Users/kushal/Desktop/New folder (10)
> 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 -694988524
> Generated 165 of the 1596 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_X'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> NOTE 2 [file topol.top, line 11469]:
>   System has non-zero total charge: 10.000000
>   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.
>
>
>
>
> -------------------------------------------------------
> Program:     gmx grompp, version 2018.1
> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 619)
>
> Fatal error:
> number of coordinates in coordinate file (solv.gro, 45034)
>              does not match topology (topol.top, 44947)
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> kushalrajroy at DESKTOP-RVURRJU:/mnt/c/Users/kushal/Desktop/New folder (10)$
> gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
>                       :-) GROMACS - gmx grompp, 2018.1 (-:
>
>                             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 grompp, version 2018.1
> Executable:   /usr/bin/gmx
> Data prefix:  /usr
> Working dir:  /mnt/c/Users/kushal/Desktop/New folder (10)
> 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 1547355040
>
> ERROR 1 [file ligand.prm, line 4]:
>   Unknown bond_atomtype CG2O2
>
>
>
> There was 1 note
>
> -------------------------------------------------------
> Program:     gmx grompp, version 2018.1
> Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 777)
>
> Fatal error:
> There was 1 error in input file(s)
> --
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