Erorr in energy minimization

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GROMACS version:2020
GROMACS modification: Yes/No
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I work on protein-ligand simulation, when running this command in energy minimization
gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr
I faced this problem, how can I fix it?

NOTE 1 [file em.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 -1588013375
Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 117519 of the 167910 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘alp’
Excluding 2 bonded neighbours molecule type ‘SOL’
Excluding 38 bonded neighbours molecule type ‘CL’

NOTE 2 [file topol.top, line 102725]:
System has non-zero total charge: -0.469988
Total charge should normally be an integer. See
Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation
for discussion on how close it should be to an integer.

WARNING 1 [file topol.top, line 102725]:
You are using Ewald electrostatics in a system with net charge. This can
lead to severe artifacts, such as ions moving into regions with low
dielectric, due to the uniform background charge. We suggest to
neutralize your system with counter ions, possibly in combination with a
physiological salt concentration.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof
Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net
Charge
J. Chem. Theory Comput. 10 (2014) pp. 381-393
-------- -------- — Thank You — -------- --------

NOTE 3 [file topol.top, line 102725]:
In moleculetype ‘Protein_chain_A’ 955 atoms are not bound by a potential
or constraint to any other atom in the same moleculetype. Although
technically this might not cause issues in a simulation, this often means
that the user forgot to add a bond/potential/constraint or put multiple
molecules in the same moleculetype definition by mistake. Run with -v to
get information for each atom.

Analysing residue names:
There are: 685 Protein residues
There are: 1 Other residues
There are: 55420 Water residues
There are: 76 Ion residues
Analysing Protein…
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
Number of degrees of freedom in T-Coupling group rest is 368205.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 120x120x120, spacing 0.114 0.114 0.114
Estimate for the relative computational load of the PME mesh part: 0.14
This run will generate roughly 14 Mb of data

There were 3 notes

There was 1 warning

Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2353)

Fatal error:
Too many warnings (1).
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 Common Errors — GROMACS webpage https://www.gromacs.org documentation

2

Here’s your problem. Likely the charges assigned to your ligand are incorrect as they should not sum to a fractional value.

3

Hi jalemkul
after I corrected this error I faced this error

I am using gromacs to energy minimize Protein-Ligand complex. I have performed all the steps as described in tutorial but i am getting this error while running grompp :
gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr
:-) GROMACS - gmx grompp, 2020.1-Ubuntu-2020.1-1 (-:

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GROMACS: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/bioinfo/alp/alph
Command line:
gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr

Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘ns_type’

NOTE 1 [file em.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 -1798595331
Generated 168379 of the 168490 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 118001 of the 168490 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘alp’
Excluding 2 bonded neighbours molecule type ‘SOL’
Excluding 3 bonded neighbours molecule type ‘NA’
Excluding 3 bonded neighbours molecule type ‘CL’
Excluding 3 bonded neighbours molecule type ‘CL’

NOTE 2 [file topol.top, line 102736]:
System has non-zero total charge: -76.469988
Total charge should normally be an integer. See
Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation
for discussion on how close it should be to an integer.

WARNING 1 [file topol.top, line 102736]:
You are using Ewald electrostatics in a system with net charge. This can
lead to severe artifacts, such as ions moving into regions with low
dielectric, due to the uniform background charge. We suggest to
neutralize your system with counter ions, possibly in combination with a
physiological salt concentration.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof
Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net
Charge
J. Chem. Theory Comput. 10 (2014) pp. 381-393
-------- -------- — Thank You — -------- --------

WARNING: Bad box in file solv_ions.gro

Generated a cubic box 15.524 x 13.978 x 10.104
Warning: atom name 177205 in topol.top and solv_ions.gro does not match (NA - OW)
Warning: atom name 177206 in topol.top and solv_ions.gro does not match (NA - HW1)
Warning: atom name 177207 in topol.top and solv_ions.gro does not match (NA - HW2)
Warning: atom name 177208 in topol.top and solv_ions.gro does not match (NA - OW)
Warning: atom name 177209 in topol.top and solv_ions.gro does not match (NA - HW1)
Warning: atom name 177210 in topol.top and solv_ions.gro does not match (NA - HW2)
Warning: atom name 177211 in topol.top and solv_ions.gro does not match (NA - OW)
Warning: atom name 177212 in topol.top and solv_ions.gro does not match (NA - HW1)
Warning: atom name 177213 in topol.top and solv_ions.gro does not match (NA - HW2)
Warning: atom name 177214 in topol.top and solv_ions.gro does not match (NA - OW)
Warning: atom name 177215 in topol.top and solv_ions.gro does not match (NA - HW1)
Warning: atom name 177216 in topol.top and solv_ions.gro does not match (NA - HW2)
Warning: atom name 177217 in topol.top and solv_ions.gro does not match (NA - OW)
Warning: atom name 177218 in topol.top and solv_ions.gro does not match (NA - HW1)
Warning: atom name 177219 in topol.top and solv_ions.gro does not match (NA - HW2)
Warning: atom name 177220 in topol.top and solv_ions.gro does not match (NA - OW)
Warning: atom name 177221 in topol.top and solv_ions.gro does not match (NA - HW1)
Warning: atom name 177222 in topol.top and solv_ions.gro does not match (NA - HW2)
Warning: atom name 177223 in topol.top and solv_ions.gro does not match (NA - OW)
Warning: atom name 177224 in topol.top and solv_ions.gro does not match (NA - HW1)
(more than 20 non-matching atom names)

WARNING 2 [file topol.top, line 102736]:
368 non-matching atom names
atom names from topol.top will be used
atom names from solv_ions.gro will be ignored

NOTE 3 [file topol.top, line 102736]:
In moleculetype ‘Protein_chain_A’ 955 atoms are not bound by a potential
or constraint to any other atom in the same moleculetype. Although
technically this might not cause issues in a simulation, this often means
that the user forgot to add a bond/potential/constraint or put multiple
molecules in the same moleculetype definition by mistake. Run with -v to
get information for each atom.

Analysing residue names:
There are: 685 Protein residues
There are: 1 Other residues
There are: 55128 Water residues
There are: 368 Ion residues
Analysing Protein…
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
Number of degrees of freedom in T-Coupling group rest is 367329.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 144x120x96, spacing 0.108 0.116 0.105
Estimate for the relative computational load of the PME mesh part: 0.16
This run will generate roughly 14 Mb of data

There were 3 notes

There were 2 warnings

Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2353)

Fatal error:
Too many warnings (2).
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 Common Errors — GROMACS webpage https://www.gromacs.org documentation

I want to ask about (177205), This number indicate the line in the file or what? and how can I fix this problem?

4

You still have the same underlying problem. You need to stop and fix the topology issue before trying to do anything. A fractional charge indicates a severe problem. Start by looking at your ligand.

You have a misformatted coordinate file.

Here, the problem is your coordinate file is out of order with respect to the topology. The contents of [molecules] must be in the same order as the coordinate file.