GROMACS version:
GROMACS modification: Yes/No
Here post your question
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.