[gmx-users] (no subject)

[Justin Lemkul]

On 9/10/18 9:14 AM, Bratin Kumar Das wrote:
> Use -maxwarn 2 at the last of your gmx grompp ... command

No! One should *never* use -maxwarn just to circumvent problems. It is 
clear that there is some modification to ffnonbonded.itp that is 
syntactically incorrect. grompp will not have the right parameters and 
any process that tries to use this .tpr file will fail.

-Justin

> 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
>>
>>
>>
>> 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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