[gmx-users] grompp error

‪Mohammad Roostaie‬ ‪ mohammad.r0325 at yahoo.com
Thu May 25 08:20:38 CEST 2017

Hi GROMACS users,

I want to simulate a graphene sheet, and I want to use OPLS-AA force field. So, I copied the forcefield in my directory and changed some the files in it (ffbonded.itp, ffnonbonded.itp, atomtype.atp, aminoacids.rtp, and atomname2type.n2t). I used the pdb2gmx command to create the first topology and coordinate files with the modified OPLS-AA forcefield, then I created a box and solvated it with water. But, when I wanted to add ions to the box by using “gmx grompp -f ions.mdp -c gr_solv.gro -p gr.top -o ions.tpr”, I got this error: 

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 209904318
WARNING 1 [file ffbonded.itp, line 305]:  Overriding Bond parameters.
  old:                                          0.151 292880 0.151 292880  new: C     C       1    0.14000   392459.2
Generated 333336 of the 333336 non-bonded parameter combinationsGenerating 1-4 interactions: fudge = 0.5Generated 333336 of the 333336 1-4 parameter combinations
-------------------------------------------------------Program gmx grompp, VERSION 5.1.4Source code file: /home/jemmyhu/work/software/gromacs/gromacs-5.1.4/src/gromacs/gmxpreprocess/topio.c, line: 755
Fatal error:Syntax error - File forcefield.itp, line 18Last line read:'[ defaults ]'Invalid order for directive defaultsFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors

Can you please help me to solve this problem?

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