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

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1

GROMACS version: version 2018.1
GROMACS modification: Yes/No
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I am getting the following error while running gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
Command line:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

Ignoring obsolete mdp entry ‘title’

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 -1429844739
Generated 100465 of the 100576 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 66298 of the 100576 1-4 parameter combinations

ERROR 1 [file unk.itp, line 94]:
No default Bond types

ERROR 2 [file unk.itp, line 292]:
No default U-B types

ERROR 3 [file unk.itp, line 298]:
No default U-B types

ERROR 4 [file unk.itp, line 324]:
No default U-B types

ERROR 5 [file unk.itp, line 331]:
No default U-B types

ERROR 6 [file unk.itp, line 334]:
No default U-B types

ERROR 7 [file unk.itp, line 335]:
No default U-B types

ERROR 8 [file unk.itp, line 419]:
No default Proper Dih. types

ERROR 9 [file unk.itp, line 422]:
No default Proper Dih. types

ERROR 10 [file unk.itp, line 460]:
No default Proper Dih. types

ERROR 11 [file unk.itp, line 467]:
No default Proper Dih. types

ERROR 12 [file unk.itp, line 476]:
No default Proper Dih. types

ERROR 13 [file unk.itp, line 484]:
No default Proper Dih. types

ERROR 14 [file unk.itp, line 485]:
No default Proper Dih. types

ERROR 15 [file unk.itp, line 488]:
No default Proper Dih. types

ERROR 16 [file unk.itp, line 495]:
No default Proper Dih. types

Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_B’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_C’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_D’
Excluding 3 bonded neighbours molecule type ‘UNK’
Excluding 2 bonded neighbours molecule type ‘SOL’

NOTE 2 [file topol.top, line 60]:
System has non-zero total charge: 16.000000
Total charge should normally be an integer. See
Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation
for discussion on how close it should be to an integer.

Removing all charge groups because cutoff-scheme=Verlet

There were 2 notes

Program: gmx grompp, version 2018.1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1991)

Fatal error:
There were 16 errors in input file(s)

Please help me in figuring this out!

2

Hii Princii,
The error means that the forcefield that you are using for generating .tpr file is not finding the bondtypes (No default U-B types) and dihedral parameters (No default proper dih. types) for the residue/chain that you are working on. While generating .tpr file, the gromacs checks for bonded and dihedral parameters in ffbonded.itp file and if it doesn’t find these parameters it give the following error.

To resolve this you can generate topology and parameter file from any external site (based on the forcefield that you want to use) like charmm gui, ATB, etc and add that parameters to your ffbonded.itp file in your forcefiled folder with exact atomnames and atomtypes that you have used in your starting pdb file.

3

Hi Rajat!
Thanks for your help. Can you tell me any external site as you mentioned. I am using charmm36-feb2021.