# An error while executing command : gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr **URL:** \ **Category:** User discussions\ **Tags:** forcefield, grompp\ **Created:** [January 27, 2022, 4:40pm UTC](https://gromacs.bioexcel.eu/t/an-error-while-executing-command-gmx-grompp-f-ions-mdp-c-solv-gro-p-topol-top-o-ions-tpr/3557 "2022-01-27T16:40:53Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![aldowanandy](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/aldowanandy/32/1167_2.png) [@aldowanandy](https://gromacs.bioexcel.eu/u/aldowanandy)\ **Post date:** [January 27, 2022, 4:40pm UTC](https://gromacs.bioexcel.eu/t/an-error-while-executing-command-gmx-grompp-f-ions-mdp-c-solv-gro-p-topol-top-o-ions-tpr/3557/1 "2022-01-27T16:40:53Z")
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](http://www.gromacs.org/Documentation/Floating_Point_Arithmetic) 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](http://www.gromacs.org/Documentation/Errors) - this is the setting I did on the web ([https://server.poissonboltzmann.org/pdb2pqr](https://server.poissonboltzmann.org/pdb2pqr))` - The forcefield I use is the CHARMM36 all-atom force field (July 2017) found in the Gromacs web tutorial - This is the link containing the file that I am trying to simulate on my laptop [https://drive.google.com/drive/folders/1TXUZ4MfrRV0qgpX2-l0bBlC0oGfx-Dxm?usp=sharing](https://drive.google.com/drive/folders/1TXUZ4MfrRV0qgpX2-l0bBlC0oGfx-Dxm?usp=sharing) ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [January 28, 2022, 11:26am UTC](https://gromacs.bioexcel.eu/t/an-error-while-executing-command-gmx-grompp-f-ions-mdp-c-solv-gro-p-topol-top-o-ions-tpr/3557/2 "2022-01-28T11:26:32Z")
> [@aldowanandy](#): > > ERROR 1 [file kni.itp, line 588]: > No default Proper Dih. types This means you have some species for which a dihedral is undefined in the force field. You need to supply parameters for it. ---
**Author:** ![aldowanandy](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/aldowanandy/32/1167_2.png) [@aldowanandy](https://gromacs.bioexcel.eu/u/aldowanandy)\ **Post date:** [January 30, 2022, 8:15am UTC](https://gromacs.bioexcel.eu/t/an-error-while-executing-command-gmx-grompp-f-ions-mdp-c-solv-gro-p-topol-top-o-ions-tpr/3557/3 "2022-01-30T08:15:25Z")
Thanks for the response sir, any suggestions on how to supply parameters for this? or any suggestion what forcefield i should use for this? ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [January 31, 2022, 11:09am UTC](https://gromacs.bioexcel.eu/t/an-error-while-executing-command-gmx-grompp-f-ions-mdp-c-solv-gro-p-topol-top-o-ions-tpr/3557/4 "2022-01-31T11:09:51Z")
[http://www.mdtutorials.com/gmx/complex/index.html](http://www.mdtutorials.com/gmx/complex/index.html) ---
**Author:** ![Shefin2022](https://avatars.discourse-cdn.com/v4/letter/s/f19dbf/32.png) [@Shefin2022](https://gromacs.bioexcel.eu/u/Shefin2022)\ **Post date:** [March 6, 2022, 9:34am UTC](https://gromacs.bioexcel.eu/t/an-error-while-executing-command-gmx-grompp-f-ions-mdp-c-solv-gro-p-topol-top-o-ions-tpr/3557/5 "2022-03-06T09:34:39Z")
@aldowanandy, do u know how to supply those parameters for these kind of errors. I got the same error. ---
**Author:** ![Shefin2022](https://avatars.discourse-cdn.com/v4/letter/s/f19dbf/32.png) [@Shefin2022](https://gromacs.bioexcel.eu/u/Shefin2022)\ **Post date:** [February 17, 2023, 6:58am UTC](https://gromacs.bioexcel.eu/t/an-error-while-executing-command-gmx-grompp-f-ions-mdp-c-solv-gro-p-topol-top-o-ions-tpr/3557/6 "2023-02-17T06:58:51Z")
> [@jalemkul](#): > > supply parameters for it. 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](http://www.mdtutorials.com/gmx/complex/index.html). But stuck in tpr generation step.