[gmx-users] (no subject)

[Neha Tiwari]

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:

     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:  /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)



For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors




Please help.
Thanks in advance.

Regards,
Neha.