Fatal error trying to use Gromacs Wizard : gro file does not have the number of atoms on the second line



  • Hello, trying to use the Gromacs Wizard to prepare a simulation based, on the tutorial founded here http://www.mdtutorials.com/gmx/lysozyme/04_ions.html. Trying to make the preparation step, generating the box, adding solvent and ions. When I click on prepare I nearly immediately got a fatal error :

    *Program: gmx editconf, version 2020.3-MODIFIED
    Source file: src\gromacs\fileio\groio.cpp (line 67)

    Fatal error:
    gro file does not have the number of atoms on the second line*

    Finding the gro file in my working directory I can find that its weight is 0 ko, and opening it with notepad, there's nothing written in.

    I try to generate a gro file with gromacs model generator and use it to replace the gro file of the working directory, but this doesn't work.

    Any idea on how to solve this ?

    Here the output file :

    ######################################## PREPARATION STARTED ########################################

             :-) GROMACS - gmx pdb2gmx, 2020.3-MODIFIED (-:
    
                        GROMACS is written by:
    

    Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
    Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
    Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
    Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
    Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
    Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
    Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
    Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
    Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
    Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
    Christian Wennberg Maarten Wolf Artem Zhmurov
    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) 2001-2019, 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 pdb2gmx, version 2020.3-MODIFIED
    Executable: C:\Users\User\AppData\Local\OneAngstrom\SAMSON-Data\1.0.0\Scratch\Elements\02407D21-0490-30BA-D20F-2E88DB100FC5\Resource\gromacs\gmx.exe
    Data prefix: C:\Program Files\Gromacs
    Working dir: C:\Users\User\AppData\Local\OneAngstrom\SAMSON-Data\1.0.0\Scratch\Elements\02407D21-0490-30BA-D20F-2E88DB100FC5\Resource\gromacs
    Command line:
    gmx pdb2gmx -f C:/Users/User/AppData/Local/OneAngstrom/SAMSON-Data/1.0.0/Scratch/GROMACS/PDB/temp.pdb -o C:/Users/User/AppData/Local/OneAngstrom/SAMSON-Data/1.0.0/Scratch/GROMACS/GeneratedFiles/1AKI_model.gro -i C:/Users/User/AppData/Local/OneAngstrom/SAMSON-Data/1.0.0/Scratch/GROMACS/GeneratedFiles/1AKI_model.itp -ff oplsaa -water spc -p C:/Users/User/AppData/Local/OneAngstrom/SAMSON-Data/1.0.0/Scratch/GROMACS/GeneratedFiles/1AKI_model.top -ignh

    Opening force field file ./oplsaa.ff/aminoacids.r2b
    All occupancy fields zero. This is probably not an X-Ray structure
    Opening force field file ./oplsaa.ff/atomtypes.atp
    Opening force field file ./oplsaa.ff/aminoacids.rtp
    Opening force field file ./oplsaa.ff/aminoacids.hdb
    Opening force field file ./oplsaa.ff/aminoacids.n.tdb
    Opening force field file ./oplsaa.ff/aminoacids.c.tdb
    Analysing hydrogen-bonding network for automated assignment of histidine
    protonation. 213 donors and 184 acceptors were found.
    There are 256 hydrogen bonds
    Will use HISE for residue 15
    8 out of 8 lines of specbond.dat converted successfully
    Special Atom Distance matrix:
    CYS6 MET12 HIS15 CYS30 CYS64 CYS76 CYS80
    SG48 SD87 NE2118 SG238 SG513 SG601 SG630
    MET12 SD87 1.167
    HIS15 NE2118 1.776 1.018
    CYS30 SG238 1.406 1.054 2.068
    CYS64 SG513 2.835 1.793 1.789 2.241
    CYS76 SG601 2.705 1.551 1.468 2.115 0.765
    CYS80 SG630 2.959 1.950 1.916 2.390 0.198 0.944
    CYS94 SG724 2.550 1.407 1.382 1.974 0.666 0.201 0.855
    MET105 SD799 1.827 0.911 1.683 0.888 1.849 1.461 2.036
    CYS115 SG889 1.577 1.084 2.078 0.200 2.111 1.989 2.262
    CYS127 SG981 0.198 1.072 1.720 1.313 2.799 2.622 2.933
    CYS94 MET105 CYS115
    SG724 SD799 SG889
    MET105 SD799 1.381
    CYS115 SG889 1.853 0.790
    CYS127 SG981 2.475 1.685 1.483
    Linking CYS-6 SG-48 and CYS-127 SG-981...
    Linking CYS-30 SG-238 and CYS-115 SG-889...
    Linking CYS-64 SG-513 and CYS-80 SG-630...
    Linking CYS-76 SG-601 and CYS-94 SG-724...
    Making bonds...
    Number of bonds was 1984, now 1984
    Generating angles, dihedrals and pairs...
    Before cleaning: 5142 pairs
    Before cleaning: 5187 dihedrals
    Keeping all generated dihedrals
    Making cmap torsions...
    There are 5187 dihedrals, 426 impropers, 3547 angles
    5106 pairs, 1984 bonds and 0 virtual sites
    Total mass 14313.193 a.m.u.
    Total charge 8.000 e
    Writing topology

    Writing coordinate file...

            :-) GROMACS - gmx editconf, 2020.3-MODIFIED (-:
    
                        GROMACS is written by:
    

    Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
    Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
    Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
    Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
    Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
    Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
    Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
    Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
    Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
    Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
    Christian Wennberg Maarten Wolf Artem Zhmurov
    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) 2001-2019, 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 editconf, version 2020.3-MODIFIED
    Executable: C:\Users\User\AppData\Local\OneAngstrom\SAMSON-Data\1.0.0\Scratch\Elements\02407D21-0490-30BA-D20F-2E88DB100FC5\Resource\gromacs\gmx.exe
    Data prefix: C:\Program Files\Gromacs
    Working dir: C:\Users\User\AppData\Local\OneAngstrom\SAMSON-Data\1.0.0\Scratch\Elements\02407D21-0490-30BA-D20F-2E88DB100FC5\Resource\gromacs
    Command line:
    gmx editconf -f C:/Users/User/AppData/Local/OneAngstrom/SAMSON-Data/1.0.0/Scratch/GROMACS/GeneratedFiles/1AKI_model.gro -o C:/Users/User/AppData/Local/OneAngstrom/SAMSON-Data/1.0.0/Scratch/GROMACS/GeneratedFiles/1AKI_boxed.gro -c -box 4.234 -bt cubic

    Program: gmx editconf, version 2020.3-MODIFIED
    Source file: src\gromacs\fileio\groio.cpp (line 67)

    Fatal error:
    gro file does not have the number of atoms on the second line

    For more information and tips for troubleshooting, please check the GROMACS
    website at http://www.gromacs.org/Documentation/Errors
    Note that major changes are planned in future for editconf, to improve usability and utility.



  • Dear Guy,

    thank you for your interest in SAMSON and the GROMACS Wizard extension. Could you please tell me whether you clicked "Compute fitted box" first, to indicate what system you want to simulate? It looks like nothing was selected, and no atoms were exported. I just did a quick test with 1AKI (the PDB indicated in the tutorial):

    • removed the waters using the document view
    • clicked Compute fitted box
    • increased the box size to 7,015nm
    • checked Add solvent and Neutralize system (using Ca and Cl)
    • clicked Prepare

    Here is what I obtain: (I added a secondary structure in the Biology menu)

    0_1613423373076_b77ff4b7-6791-4d88-81f1-ba137a9d60fe-image.png

    If you'd like, you can use the 1AKI tutorial adapted for the GROMACS Wizard: https://documentation.samson-connect.net/gromacs-wizard/. Please let us know if you have any questions.

    thanks,
    best,

    Stephane



  • The 1AKI pdb file was imported and cleaned of all the water molecules.

    I didn't increase the sized of the box and it was a 4,115 nm box. Add solvent and Neutralize system was selected using Na and Cl. Then after clicking on prepare I got the file reported in my first post.

    I used the oplsaa forcefield with the spc water model. I also give a try to your parameter (amber03 instead of oplsaa, tip3p instead of spc, and Ca instead of Na). But this lead me to the same result.

    If I try to generate a gro file using the Model Generator, it generate one file but this one doesn't work for all the other calculations.

    Here is my screen :

    0_1613424650992_2e6955ea-490e-4b1f-988c-61cf291f95f9-image.png



  • Could you please tell me whether you added custom force fields? (Using the + sign). If yes, please try to remove them (using the X sign) and try again, and let me know.
    Thanks,
    Stephane



  • No, I just have the force fields provided with the extension. Even though I tried removing with the X sign, no change.
    Thanks for your help



  • Ok thanks. I'm going to contact you by email for further exchange.


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