Error in (gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr)

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1

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This is the error I keep getting:

Here is everything about the error from the terminal:

Executable: /opt/homebrew/bin/…/Cellar/gromacs/2024.3/bin/gmx

Data prefix: /opt/homebrew/bin/…/Cellar/gromacs/2024.3

Working dir: /Users/arneshbanerjee/Downloads

Command line:

gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

Ignoring obsolete mdp entry ‘title’

Ignoring obsolete mdp entry ‘ns_type’

Setting the LD random seed to 2046558205

Generated 330891 of the 330891 non-bonded parameter combinations

Generating 1-4 interactions: fudge = 0.5

Generated 330891 of the 330891 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’

Excluding 3 bonded neighbours molecule type ‘Protein_chain_B’

Excluding 2 bonded neighbours molecule type ‘SOL’

NOTE 1 [file topol.top, line 50]:

System has non-zero total charge: -33.000000

Total charge should normally be an integer. See

Floating point arithmetic - GROMACS 2025.1 documentation

for discussion on how close it should be to an integer.

atom name 27 in topol.top and solv.gro does not match (OG - CG)

atom name 27 in topol.top and solv.gro does not match (OG - CG)

atom name 28 in topol.top and solv.gro does not match (HG - HG1)

atom name 28 in topol.top and solv.gro does not match (HG - HG1)

atom name 29 in topol.top and solv.gro does not match (C - HG2)

atom name 29 in topol.top and solv.gro does not match (C - HG2)

atom name 30 in topol.top and solv.gro does not match (O - SD)

atom name 30 in topol.top and solv.gro does not match (O - SD)

atom name 31 in topol.top and solv.gro does not match (N - CE)

atom name 31 in topol.top and solv.gro does not match (N - CE)

atom name 32 in topol.top and solv.gro does not match (H - HE1)

atom name 32 in topol.top and solv.gro does not match (H - HE1)

atom name 33 in topol.top and solv.gro does not match (CA - HE2)

atom name 33 in topol.top and solv.gro does not match (CA - HE2)

atom name 34 in topol.top and solv.gro does not match (HA - HE3)

atom name 34 in topol.top and solv.gro does not match (HA - HE3)

atom name 35 in topol.top and solv.gro does not match (CB - C)

atom name 35 in topol.top and solv.gro does not match (CB - C)

atom name 36 in topol.top and solv.gro does not match (HB1 - O)

atom name 36 in topol.top and solv.gro does not match (HB1 - O)

atom name 37 in topol.top and solv.gro does not match (HB2 - N)

atom name 37 in topol.top and solv.gro does not match (HB2 - N)

atom name 38 in topol.top and solv.gro does not match (CG - H)

atom name 38 in topol.top and solv.gro does not match (CG - H)

atom name 39 in topol.top and solv.gro does not match (HG1 - CA)

atom name 39 in topol.top and solv.gro does not match (HG1 - CA)

atom name 40 in topol.top and solv.gro does not match (HG2 - HA)

atom name 40 in topol.top and solv.gro does not match (HG2 - HA)

atom name 41 in topol.top and solv.gro does not match (CD - CB)

atom name 41 in topol.top and solv.gro does not match (CD - CB)

atom name 42 in topol.top and solv.gro does not match (HD1 - HB1)

atom name 42 in topol.top and solv.gro does not match (HD1 - HB1)

atom name 43 in topol.top and solv.gro does not match (HD2 - HB2)

atom name 43 in topol.top and solv.gro does not match (HD2 - HB2)

atom name 44 in topol.top and solv.gro does not match (CE - CG)

atom name 44 in topol.top and solv.gro does not match (CE - CG)

atom name 45 in topol.top and solv.gro does not match (HE1 - HG1)

atom name 45 in topol.top and solv.gro does not match (HE1 - HG1)

atom name 46 in topol.top and solv.gro does not match (HE2 - HG2)

atom name 46 in topol.top and solv.gro does not match (HE2 - HG2)

(more than 20 non-matching atom names)

(more than 20 non-matching atom names)

WARNING 1 [file topol.top, line 50]:

12086 non-matching atom names

atom names from topol.top will be used

atom names from solv.gro will be ignored

Analysing residue names:

There are: 796 Protein residues

There are: 362779 Water residues

Analysing Protein…

Number of degrees of freedom in T-Coupling group rest is 2214396.00

The integrator does not provide a ensemble temperature, there is no
system ensemble temperature

NOTE 2 [file ions.mdp]:

You are using a plain Coulomb cut-off, which might produce artifacts.

You might want to consider using PME electrostatics.

This run will generate roughly 84 Mb of data

There were 2 NOTEs

There was 1 WARNING

Program: gmx grompp, version 2024.3-Homebrew

Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2751)

Fatal error:

Too many warnings (1).

If you are sure all warnings are harmless, use the -maxwarn option.

2

Try running with -maxwarn option and you would get all the warnings while your ion addition would go good.

gmx grompp -f ions.tpr -c solv.gro -p topol.top -o ions.tpr -maxwarn 3

Typically, this results from net charge of the system. It also looks like you have some atom name mis-match.

3

Thank you so much for your reply.

I tried using the -maxwarn 3 option however the match error persists.

Fatal error:
number of coordinates in coordinate file (solv.gro, 1100912)
does not match topology (topol.top, 4365923)

Could you possibly direct me in how to solve it without maxwarn? I am very new to GROMACS. I would really appreciate it. Thank you

4

In general you should not use the -maxwarn option, especially for mismatching of atom names! One exception is the presence of net charge when you compile the tpr file for adding ions, but that is only in one passage and needs a -maxwarn 1, which also is probably not needed anymore in newer GROMACS versions (in fact you get a NOTE not a WARNING).

The main problem here is that you have mismatching atoms names, and the topology is not describing correctly the box, as the box has 1100912 atoms while the topology has 4365923. I would go back to the process of the generation of the box and check what went wrong there.

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