[gmx-users] (no subject)

[Bratin Kumar Das]

Use -maxwarn 2 at the last of your gmx grompp ... command

On Mon, Sep 10, 2018, 6:19 PM saranya <saranyahoney17 at 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
>
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> 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
> --
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