# Error parameters for dihedral type 9 **URL:** \ **Category:** User discussions\ **Created:** [December 4, 2025, 12:35am UTC](https://gromacs.bioexcel.eu/t/error-parameters-for-dihedral-type-9/13000 "2025-12-04T00:35:15Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![nthpham](https://avatars.discourse-cdn.com/v4/letter/n/e480ec/32.png) [@nthpham](https://gromacs.bioexcel.eu/u/nthpham)\ **Post date:** [December 4, 2025, 12:35am UTC](https://gromacs.bioexcel.eu/t/error-parameters-for-dihedral-type-9/13000/1 "2025-12-04T00:35:15Z")
GROMACS version:2024 GROMACS modification: Yes/No Hello, I followed all the instruction of tutorial of GROMACS to setup MD similation for protein with my ligand. However, during the 1st step of adding ion, when I run this command lines gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr I encountered these error 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 1966243839 ERROR 1 [file mbp.prm, line 25]: Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported. ERROR 2 [file mbp.prm, line 26]: Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported. ERROR 3 [file mbp.prm, line 27]: Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported. ERROR 4 [file mbp.prm, line 30]: Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported. ERROR 5 [file mbp.prm, line 31]: Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported. ERROR 6 [file mbp.prm, line 32]: Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported. ERROR 7 [file mbp.prm, line 35]: Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported. ERROR 8 [file mbp.prm, line 36]: Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported. ERROR 9 [file mbp.prm, line 37]: Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported. ERROR 10 [file mbp.prm, line 38]: Encountered a second block of parameters for dihedral type 9 for the same atoms, with either different parameters and/or the first block has multiple lines. This is not supported. Generated 167799 of the 167910 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 117432 of the 167910 1-4 parameter combinations ERROR 11 [file mbp.itp, line 5]: moleculetype MBP is redefined There was 1 NOTE ------------------------------------------------------- Program: gmx grompp, version 2024.4-EasyBuild\_4.9.4 Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1518) Fatal error: There were 11 errors in input file(s) Can anyone give me instructions or suggestions how to fix it ? Thanks ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [December 4, 2025, 3:07pm UTC](https://gromacs.bioexcel.eu/t/error-parameters-for-dihedral-type-9/13000/2 "2025-12-04T15:07:40Z")
This looks like an issue caused by the force field files. What forcefield are you using and where did you get the files from? ---
**Author:** ![nthpham](https://avatars.discourse-cdn.com/v4/letter/n/e480ec/32.png) [@nthpham](https://gromacs.bioexcel.eu/u/nthpham)\ **Post date:** [December 4, 2025, 3:38pm UTC](https://gromacs.bioexcel.eu/t/error-parameters-for-dihedral-type-9/13000/3 "2025-12-04T15:38:47Z")
I used charmm36-jul2022.ff ---
**Author:** ![nthpham](https://avatars.discourse-cdn.com/v4/letter/n/e480ec/32.png) [@nthpham](https://gromacs.bioexcel.eu/u/nthpham)\ **Post date:** [December 4, 2025, 4:01pm UTC](https://gromacs.bioexcel.eu/t/error-parameters-for-dihedral-type-9/13000/4 "2025-12-04T16:01:56Z")
I got the .str file from [CGFEN](https://cgenff.com/) server after upload .mol2 file. Then I follow the instruction to use this command line to get mbp\_ini.pdb mbp.prm mbp.top mbp.itp file python cgenff\_charmm2gmx.py MBP MBP\_fix.mol2 MBP.str charmm36-jul2022.ff ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [December 5, 2025, 7:27am UTC](https://gromacs.bioexcel.eu/t/error-parameters-for-dihedral-type-9/13000/5 "2025-12-05T07:27:58Z")
I have never used cgfen, so I don’t know how this works. The charmm36-jul2022.ff package does not contain an mbp.prm file. There is clearly an issue in the mbp.prm file. Maybe you are lucky that the combination of atom types for this dihedral do not occur in your system, then you can remove the problematic lines. ---
**Author:** ![nthpham](https://avatars.discourse-cdn.com/v4/letter/n/e480ec/32.png) [@nthpham](https://gromacs.bioexcel.eu/u/nthpham)\ **Post date:** [December 5, 2025, 6:24pm UTC](https://gromacs.bioexcel.eu/t/error-parameters-for-dihedral-type-9/13000/6 "2025-12-05T18:24:16Z")
Hi Hess, I found the issue. It turns out that there is double line of include ligand in my topology file that causes the issues. I remove the duplicate line. It’s good now.