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@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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