# Error while running gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr **URL:** \ **Category:** User discussions\ **Created:** [July 5, 2022, 8:17am UTC](https://gromacs.bioexcel.eu/t/error-while-running-gmx-grompp-f-ions-mdp-c-solv-gro-p-topol-top-o-ions-tpr/4410 "2022-07-05T08:17:29Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![Princii](https://avatars.discourse-cdn.com/v4/letter/p/439d5e/32.png) [@Princii](https://gromacs.bioexcel.eu/u/Princii)\ **Post date:** [July 5, 2022, 8:17am UTC](https://gromacs.bioexcel.eu/t/error-while-running-gmx-grompp-f-ions-mdp-c-solv-gro-p-topol-top-o-ions-tpr/4410/1 "2022-07-05T08:17:29Z")
GROMACS version: version 2018.1 GROMACS modification: Yes/No Here post your question 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](http://www.gromacs.org/Documentation/Floating_Point_Arithmetic) 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! ---
**Author:** ![Rajat](https://avatars.discourse-cdn.com/v4/letter/r/ebca7d/32.png) [@Rajat](https://gromacs.bioexcel.eu/u/Rajat)\ **Post date:** [July 5, 2022, 9:16am UTC](https://gromacs.bioexcel.eu/t/error-while-running-gmx-grompp-f-ions-mdp-c-solv-gro-p-topol-top-o-ions-tpr/4410/2 "2022-07-05T09:16:07Z")
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. ---
**Author:** ![Princii](https://avatars.discourse-cdn.com/v4/letter/p/439d5e/32.png) [@Princii](https://gromacs.bioexcel.eu/u/Princii)\ **Post date:** [July 9, 2022, 4:03pm UTC](https://gromacs.bioexcel.eu/t/error-while-running-gmx-grompp-f-ions-mdp-c-solv-gro-p-topol-top-o-ions-tpr/4410/3 "2022-07-09T16:03:36Z")
Hi Rajat! Thanks for your help. Can you tell me any external site as you mentioned. I am using charmm36-feb2021.