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

User discussions
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1

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

2

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

3

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

4

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

5

@aldowanandy,

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

6

Sir, Can you please tell me how to add parameters for undefined species in .itp file. I have used Charmm force field. I am stuck here. I strictly followed the wonderful tutorial. Protein-Ligand Complex. But stuck in tpr generation step.