An error while executing command : gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

GROMACS version: 2020.1
GROMACS modification: No

I encountered an error message like this while running the adding ions step, previously I used the pdb2pqr server to change the pH of my protein.pdb . I want to do a molecular dynamics simulation with variations in protein pH, in the hope of getting different rmsd results for each pH variation. Thank you in advance

  • 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’

NOTE 1 [file ions.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 407718296
Generated 100032 of the 100128 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 65937 of the 100128 1-4 parameter combinations

ERROR 1 [file kni.itp, line 588]:
No default Proper Dih. types

Excluding 3 bonded neighbours molecule type ‘Protein’
Excluding 3 bonded neighbours molecule type ‘KNI’
Excluding 2 bonded neighbours molecule type ‘SOL’

NOTE 2 [file topol.top, line 47795]:
System has non-zero total charge: -11.000000
Total charge should normally be an integer. See
GROMACS - Gromacs
for discussion on how close it should be to an integer.

There were 2 notes


Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1928)

Fatal error:
There was 1 error in input file(s)

For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs

This means you have some species for which a dihedral is undefined in the force field. You need to supply parameters for it.

Thanks for the response sir, any suggestions on how to supply parameters for this? or any suggestion what forcefield i should use for this?

http://www.mdtutorials.com/gmx/complex/index.html

@aldowanandy,

do u know how to supply those parameters for these kind of errors.
I got the same error.