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, <kushalrajro...@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@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) > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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