[gmx-users] Can you help regarding this

[Kushal Roy]

                            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)