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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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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