[gmx-users] (no subject)

saranya saranyahoney17 at gmail.com
Mon Sep 10 14:48:10 CEST 2018

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 (-:

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 Dimitrios Karkoulis    Peter Kasson        Jiri Kraus      Carsten Kutzner

    Per Larsson      Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff

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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


  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


  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:
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,


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