Getting A Fatal Error from Gromacs

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Hi Guys,

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

I typed the following command shown above into Gromacs but I get the following script regarding an error.

  1. NOTE 1 [file ions.mdp]:

  2. 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.

  3. Setting the LD random seed to -1774430464

  4. Generated 168 of the 1653 non-bonded parameter combinations

  5. ERROR 1 [file topol_Protein_chain_A.itp, line 1185]:

  6. No default Proper Dih. types

  7. Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’

  8. Excluding 3 bonded neighbours molecule type ‘Protein_chain_B’

  9. Excluding 2 bonded neighbours molecule type ‘SOL’

  10. WARNING 1 [file topol.top, line 48]: The GROMOS force fields have been parametrized with a physically incorrect multiple-time-stepping scheme for a twin-range cut-off. When used with a single-range cut-off (or a correct Trotter multiple-time-stepping scheme), physical properties, such as the density, might differ from the intended values. Since there are researchers actively working on validating GROMOS with modern integrators we have not yet removed the GROMOS force fields, but you should be aware of these issues and check if molecules in your system are affected before proceeding. Further information is available at https://redmine.gromacs.org/issues/2884 , and a longer explanation of our decision to remove physically incorrect algorithms can be found - https://doi.org/10.26434/chemrxiv.11474583.v1 .

  11. NOTE 2 [file topol.top, line 48]: System has non-zero total charge: 2.000000 Total charge should normally be an integer.
    See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer.

  12. There were 2 notes

  13. There was 1 warning

I have used the maxwarn option and then proceed with the following command shown below but it does not work as I have not generated by ions.tpr file.

gmx genion -s ions.tpr -o insulin_solv_ions.gro -p topol.top -pname NA -nname CL -neutral

Any solution to this problem would be much appreciated.

2

What set of atoms in a protein topology has an unknown dihedral? This is your problem that requires fixing. You can’t -maxwarn your way out of an error.

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ERROR 1 [file topol_Protein_chain_A.itp, line 1183]:
No default Proper Dih. types

ERROR 2 [file topol_Protein_chain_A.itp, line 1184]:
No default Proper Dih. types

Under the [dihedral] section it has ai, aj, ak, al, funct and c0.

At line 1183 and 1184 under c0 - I have a missing set of values. All of the values have gd_(value) but in these two lines it is missing.

NOTE 2 [file topol.top, line 48]:
System has non-zero total charge: 4.000000
Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.

At line 48 under topol.top - it shows the number of water molecules - SOL 6435

How do I overcome these issues?

4

You still didn’t answer the question - which atoms are in the missing interactions? Missing gd_* parameters suggest the force field specifies an interaction for which it does not have parameters, which seems odd and wrong.