Use -maxwarn 2 at the last of your gmx grompp ... command On Mon, Sep 10, 2018, 6:19 PM saranya <saranyahone...@gmail.com> wrote:
> Dear Users, > > My simulation system is Amyloid β Protein (1-42) with Fe2+ complex > and i am using OPLSAA forcefield for the simulations. I edited the > ffbonded.itp files accordingly as mentioned in the tutorials. > > While running grompp command, I get following error: > > > > gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr > > :-) GROMACS - gmx grompp, VERSION 5.1.2 (-: > > > > GROMACS is written by: > > Emile Apol Rossen Apostolov Herman J.C. Berendsen Par > Bjelkmar > > Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch > > Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent > Hindriksen > > Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner > > Per Larsson Justin A. Lemkul 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) 2001-2015, 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 5.1.2 > > Executable: /usr/local/gromacs/bin/gmx > > Data prefix: /usr/local/gromacs > > Command line: > > gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr > > > > Ignoring obsolete mdp entry 'title' > > > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# > > Setting the LD random seed to 2295799000 > > > > WARNING 1 [file ffnonbonded.itp, line 3]: > > Too few parameters on line (source file > > /home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c, > > line 283) > > > > Generated 335790 of the 335790 non-bonded parameter combinations > > Generating 1-4 interactions: fudge = 0.5 > > Generated 335790 of the 335790 1-4 parameter combinations > > Excluding 3 bonded neighbours molecule type 'Protein_chain_A' > > Excluding 2 bonded neighbours molecule type 'SOL' > > > > NOTE 1 [file c5.top, line 5912]: > > System has non-zero total charge: -2.000000 > > 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 > > Analysing residue names: > > There are: 42 Protein residues > > There are: 1 Other residues > > There are: 8015 Water residues > > Analysing Protein... > > Analysing residues not classified as Protein/DNA/RNA/Water and splitting > into groups... > > Number of degrees of freedom in T-Coupling group rest is 49971.00 > > Calculating fourier grid dimensions for X Y Z > > Using a fourier grid of 56x56x56, spacing 0.113 0.113 0.113 > > Estimate for the relative computational load of the PME mesh part: 0.23 > > This run will generate roughly 2 Mb of data > > > > There was 1 note > > > > There was 1 warning > > > > ------------------------------------------------------- > > Program gmx grompp, VERSION 5.1.2 > > Source code file: > /home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c, > line: 2107 > > > > Fatal error: > > Too many warnings (1), gmx terminated. > > If you are sure all warnings are harmless, use the -maxwarn option. > > For more information and tips for troubleshooting, please check the GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > ------------------------------------------------------- > > > > Anyone can help me in overcoming this fatal error will be appreciated. > > > > > > With Regards, > > Saranya Vasudevan, > > Research Scholar, > > Molecular Quantum Mechanics Laboratory, > > Department of Physics, > > Bharathiar University, > > Coimbatore-46 > -- > 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? 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.