# Error while generating tpr files
**URL:** https://gromacs.bioexcel.eu/t/error-while-generating-tpr-files/6430
**Category:** User discussions
**Tags:** forcefield, grompp
**Created:** [May 17, 2023, 7:13pm UTC](https://gromacs.bioexcel.eu/t/error-while-generating-tpr-files/6430 "2023-05-17T19:13:12Z")
**Posts on this page:** 11
**Page:** 1
### Author:  [@Tanvir](https://gromacs.bioexcel.eu/u/Tanvir)
#### Post date: [May 17, 2023, 7:13pm UTC](https://gromacs.bioexcel.eu/t/error-while-generating-tpr-files/6430/1 "2023-05-17T19:13:12Z")
GROMACS version:21
I ran the following command .And subsequent error occurred . Please help to fix it.
gmx grompp -f ions.mdp -c prot\_solv.gro -p topol.top -o ions.tpr
ERROR 1 [file unk.prm, line 8]:
Unknown bond\_atomtype CG2R64
---
### Author:  [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)
#### Post date: [May 18, 2023, 1:10pm UTC](https://gromacs.bioexcel.eu/t/error-while-generating-tpr-files/6430/2 "2023-05-18T13:10:10Z")
Hi,
Error says that in the line 8 of unk.prm file there is a wrong/unknow definition for a bond. That means that probably something is unk.prm, but it is not defined in the force field files.
If you search in the forum for ‘Unknown bond\_atomtype’ will find several posts/discussions addressing the problem and the possible solutions
[https://gromacs.bioexcel.eu/search?q=unknown%20bond\_atomtype](https://gromacs.bioexcel.eu/search?q=unknown%20bond_atomtype)
I hope it helps
Alessandra
---
### Author:  [@Tanvir](https://gromacs.bioexcel.eu/u/Tanvir)
#### Post date: [May 19, 2023, 3:36pm UTC](https://gromacs.bioexcel.eu/t/error-while-generating-tpr-files/6430/3 "2023-05-19T15:36:52Z")
python3 cgenff\_charmm2gmx\_py3\_nx2.py UNK unk\_fix.mol2 unk.str charmm36-jul2022.ff
This is the code that generated necessary files associated with ligand . i have used used the recent scripts . Tried everything i can but still found no solution.
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [May 19, 2023, 5:10pm UTC](https://gromacs.bioexcel.eu/t/error-while-generating-tpr-files/6430/4 "2023-05-19T17:10:18Z")
Please upload the `.prm` file or copy its contents here. CG2R64 has been part of CGenFF for a long time so it should certainly be supported in the July 2022 force field port.
---
### Author:  [@Tanvir](https://gromacs.bioexcel.eu/u/Tanvir)
#### Post date: [May 19, 2023, 6:52pm UTC](https://gromacs.bioexcel.eu/t/error-while-generating-tpr-files/6430/5 "2023-05-19T18:52:52Z")
Thank you for your quick comment. I’ve already mentioned the scripts I’ve used. I have considered every suggestion made in this regard. I suspected there could be a problem with my ligand. So I attempted another compound.
While the first error was associated with Unknown bond\_atomtype CG2R64,
the second error was associated with Unknown bond\_atomtype CG301.
I am sending both of the .prm files. i have named them according to their aforementioned error .
---
### Author:  [@Tanvir](https://gromacs.bioexcel.eu/u/Tanvir)
#### Post date: [May 19, 2023, 6:57pm UTC](https://gromacs.bioexcel.eu/t/error-while-generating-tpr-files/6430/6 "2023-05-19T18:57:20Z")
unk\_1.prm
ERROR 1 [file unk.prm, line 8]:
Unknown bond\_atomtype CG2R64
[bondtypes]
; i j func b0 kb
[angletypes]
; i j k func theta0 ktheta ub0 kub
CG2R64 CG2R61 CG2R64 5 115.500000 334.720000 0.24162000 29288.00
CG2R61 CG321 NG301 5 109.000000 610.864000 0.00000000 0.00
CG321 NG301 CG331 5 112.000000 585.760000 0.00000000 0.00
[dihedraltypes]
; i j k l func phi0 kphi mult
CG2R61 CG2O1 NG2S1 CG311 9 0.000000 6.694400 1
CG2R61 CG2O1 NG2S1 CG311 9 180.000000 16.736000 2
OG311 CG2O2 CG321 CG321 9 180.000000 0.000000 6
CG321 CG2R61 CG2R61 NG2R62 9 180.000000 4.184000 2
CG2R64 CG2R61 CG2R64 NG2R62 9 180.000000 5.020800 2
CG2R64 CG2R61 CG2R64 NG2S3 9 180.000000 8.368000 2
NG2R60 CG2R61 CG2R64 NG2S3 9 180.000000 20.920000 2
CG2R61 CG2R61 CG321 NG301 9 180.000000 4.184000 2
NG2R60 CG2R61 CG321 NG301 9 180.000000 0.962320 2
CG2R61 CG321 NG301 CG2R61 9 180.000000 8.368000 1
CG2R61 CG321 NG301 CG2R61 9 180.000000 1.255200 3
CG2R61 CG321 NG301 CG331 9 180.000000 3.347200 1
CG2R61 CG321 NG301 CG331 9 0.000000 2.092000 2
CG2R61 CG321 NG301 CG331 9 0.000000 2.928800 3
HGA2 CG321 NG301 CG331 9 0.000000 0.418400 3
HGA3 CG331 NG301 CG321 9 180.000000 0.000000 3
[dihedraltypes]
; ‘improper’ dihedrals
; i j k l func phi0 kphi
---
### Author:  [@Tanvir](https://gromacs.bioexcel.eu/u/Tanvir)
#### Post date: [May 19, 2023, 6:58pm UTC](https://gromacs.bioexcel.eu/t/error-while-generating-tpr-files/6430/7 "2023-05-19T18:58:13Z")
unk\_2.prm
ERROR 1 [file unk.prm, line 4]:
Unknown bond\_atomtype CG301
[bondtypes]
; i j func b0 kb
CG301 CG3RC1 1 0.15240000 186188.00
[angletypes]
; i j k func theta0 ktheta ub0 kub
CG2R53 CG2R51 CG321 5 130.000000 167.360000 0.00000000 0.00
CG311 CG2R51 CG3C52 5 119.830000 379.488800 0.00000000 0.00
CG311 CG301 CG3RC1 5 103.700000 446.432800 0.25610000 6694.40
CG321 CG301 CG3RC1 5 103.700000 446.432800 0.25610000 6694.40
CG331 CG301 CG3RC1 5 103.700000 446.432800 0.25610000 6694.40
CG2R51 CG311 CG301 5 114.000000 488.272800 0.00000000 0.00
CG2R51 CG311 CG321 5 114.000000 488.272800 0.00000000 0.00
CG331 CG311 CG3RC1 5 103.700000 446.432800 0.25610000 6694.40
CG3RC1 CG311 CG3RC1 5 103.700000 446.432800 0.25610000 6694.40
CG311 CG321 CG3RC1 5 111.000000 446.432800 0.25610000 6694.40
CG301 CG3RC1 CG3RC1 5 108.000000 446.432800 0.25610000 6694.40
CG301 CG3RC1 OG3C31 5 115.500000 505.008800 0.00000000 0.00
CG311 CG3RC1 CG311 5 113.500000 488.272800 0.25610000 9338.69
CG311 CG3RC1 OG3C31 5 115.500000 505.008800 0.00000000 0.00
CG321 CG3RC1 OG3C31 5 115.500000 505.008800 0.00000000 0.00
CG3RC1 CG3RC1 CG3RC1 5 109.000000 418.400000 0.00000000 0.00
[dihedraltypes]
; i j k l func phi0 kphi mult
CG2R53 CG2R51 CG2R51 CG311 9 180.000000 17.991200 2
CG311 CG2R51 CG2R51 CG321 9 180.000000 8.368000 2
CG321 CG2R51 CG2R53 OG2D1 9 180.000000 0.000000 2
CG321 CG2R51 CG2R53 OG3C51 9 180.000000 37.195760 2
CG2R51 CG2R51 CG311 CG301 9 0.000000 0.836800 1
CG2R51 CG2R51 CG311 CG301 9 0.000000 1.129680 2
CG2R51 CG2R51 CG311 CG301 9 0.000000 0.000000 3
CG2R51 CG2R51 CG311 CG321 9 0.000000 0.836800 1
CG2R51 CG2R51 CG311 CG321 9 0.000000 1.129680 2
CG2R51 CG2R51 CG311 CG321 9 0.000000 0.000000 3
CG3C52 CG2R51 CG311 CG301 9 0.000000 0.836800 1
CG3C52 CG2R51 CG311 CG301 9 0.000000 1.129680 2
CG3C52 CG2R51 CG311 CG301 9 0.000000 0.000000 3
CG3C52 CG2R51 CG311 CG321 9 0.000000 0.836800 1
CG3C52 CG2R51 CG311 CG321 9 0.000000 1.129680 2
CG3C52 CG2R51 CG311 CG321 9 0.000000 0.000000 3
CG3C52 CG2R51 CG311 HGA1 9 0.000000 1.807906 3
CG2R53 CG2R51 CG321 CG321 9 0.000000 0.836800 1
CG2R53 CG2R51 CG321 CG321 9 0.000000 1.129680 2
CG2R53 CG2R51 CG321 HGA2 9 0.000000 0.000000 3
CG311 CG2R51 CG3C52 OG3C51 9 0.000000 2.718763 3
CG311 CG2R51 CG3C52 HGA2 9 180.000000 4.618718 3
CG321 CG301 CG311 CG2R51 9 0.000000 0.167360 3
CG331 CG301 CG311 CG2R51 9 0.000000 0.167360 3
CG3RC1 CG301 CG311 CG2R51 9 0.000000 0.167360 3
CG3RC1 CG301 CG311 CG321 9 0.000000 0.627600 3
CG3RC1 CG301 CG311 HGA1 9 0.000000 0.627600 3
CG3RC1 CG301 CG321 CG321 9 0.000000 0.627600 3
CG3RC1 CG301 CG321 HGA2 9 0.000000 0.627600 3
CG3RC1 CG301 CG331 HGA3 9 0.000000 0.836800 3
CG311 CG301 CG3RC1 CG3RC1 9 0.000000 0.627600 3
CG311 CG301 CG3RC1 OG3C31 9 180.000000 1.966480 1
CG311 CG301 CG3RC1 OG3C31 9 0.000000 0.543920 3
CG321 CG301 CG3RC1 CG3RC1 9 0.000000 0.627600 3
CG321 CG301 CG3RC1 OG3C31 9 180.000000 1.966480 1
CG321 CG301 CG3RC1 OG3C31 9 0.000000 0.543920 3
CG331 CG301 CG3RC1 CG3RC1 9 0.000000 0.627600 3
CG331 CG301 CG3RC1 OG3C31 9 180.000000 1.966480 1
CG331 CG301 CG3RC1 OG3C31 9 0.000000 0.543920 3
CG2R51 CG311 CG321 CG3RC1 9 0.000000 0.167360 3
CG2R51 CG311 CG321 HGA2 9 0.000000 0.836800 3
CG301 CG311 CG321 CG3RC1 9 0.000000 0.836800 3
HGA1 CG311 CG321 CG3RC1 9 0.000000 0.627600 3
CG3RC1 CG311 CG331 HGA3 9 0.000000 0.836800 3
CG331 CG311 CG3RC1 CG311 9 0.000000 0.209200 3
CG331 CG311 CG3RC1 CG3RC1 9 0.000000 0.627600 3
CG331 CG311 CG3RC1 OG3C31 9 180.000000 1.966480 1
CG331 CG311 CG3RC1 OG3C31 9 0.000000 0.543920 3
CG3RC1 CG311 CG3RC1 CG311 9 0.000000 0.209200 3
CG3RC1 CG311 CG3RC1 CG3RC1 9 0.000000 0.627600 3
CG3RC1 CG311 CG3RC1 OG3C31 9 180.000000 1.966480 1
CG3RC1 CG311 CG3RC1 OG3C31 9 0.000000 0.543920 3
OG311 CG311 CG3RC1 CG311 9 0.000000 0.661072 3
OG311 CG311 CG3RC1 OG3C31 9 180.000000 14.225600 1
HGA1 CG311 CG3RC1 CG311 9 0.000000 0.209200 3
HGA1 CG311 CG3RC1 OG3C31 9 0.000000 0.669440 3
CG2R51 CG321 CG321 CG301 9 0.000000 0.167360 3
CG311 CG321 CG3RC1 CG3RC1 9 0.000000 0.627600 3
CG311 CG321 CG3RC1 OG3C31 9 180.000000 1.966480 1
CG311 CG321 CG3RC1 OG3C31 9 0.000000 0.543920 3
CG311 CG321 CG3RC1 HGA1 9 0.000000 0.627600 3
HGA2 CG321 CG3RC1 OG3C31 9 0.000000 0.669440 3
CG301 CG3RC1 CG3RC1 CG311 9 0.000000 0.627600 3
CG301 CG3RC1 CG3RC1 CG3RC1 9 0.000000 0.627600 3
CG301 CG3RC1 CG3RC1 OG3C31 9 0.000000 2.092000 4
CG301 CG3RC1 CG3RC1 HGA1 9 0.000000 0.627600 3
CG311 CG3RC1 CG3RC1 CG3RC1 9 0.000000 0.627600 3
CG311 CG3RC1 CG3RC1 OG3C31 9 0.000000 2.092000 4
CG321 CG3RC1 CG3RC1 CG3RC1 9 0.000000 0.627600 3
CG321 CG3RC1 CG3RC1 OG3C31 9 0.000000 2.092000 4
CG3RC1 CG3RC1 CG3RC1 CG3RC1 9 0.000000 0.627600 3
CG3RC1 CG3RC1 CG3RC1 OG3C31 9 0.000000 2.092000 4
CG3RC1 CG3RC1 CG3RC1 HGA1 9 0.000000 0.627600 3
OG3C31 CG3RC1 CG3RC1 OG3C31 9 0.000000 2.092000 4
CG301 CG3RC1 OG3C31 CG3RC1 9 180.000000 10.250800 3
CG301 CG3RC1 OG3C31 CG3RC1 9 0.000000 4.184000 4
CG311 CG3RC1 OG3C31 CG3RC1 9 180.000000 10.250800 3
CG311 CG3RC1 OG3C31 CG3RC1 9 0.000000 4.184000 4
CG321 CG3RC1 OG3C31 CG3RC1 9 180.000000 10.250800 3
CG321 CG3RC1 OG3C31 CG3RC1 9 0.000000 4.184000 4
CG3RC1 CG3RC1 OG3C31 CG3RC1 9 180.000000 10.250800 3
CG3RC1 CG3RC1 OG3C31 CG3RC1 9 0.000000 4.184000 4
[dihedraltypes]
; ‘improper’ dihedrals
; i j k l func phi0 kphi
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [May 19, 2023, 7:19pm UTC](https://gromacs.bioexcel.eu/t/error-while-generating-tpr-files/6430/8 "2023-05-19T19:19:38Z")
> [@Tanvir](#):
>
> While the first error was associated with Unknown bond\_atomtype CG2R64,
> the second error was associated with Unknown bond\_atomtype CG301.
You are using these ligands in concert with the CHARMM36 force field, right? Can you upload an example system topology (`.top` file) that triggers one of these errors?
---
### Author:  [@Tanvir](https://gromacs.bioexcel.eu/u/Tanvir)
#### Post date: [May 19, 2023, 7:36pm UTC](https://gromacs.bioexcel.eu/t/error-while-generating-tpr-files/6430/9 "2023-05-19T19:36:07Z")
[topol.top](https://gromacs.bioexcel.eu/uploads/short-url/fx8hDkmayQuiQaebNLhWqYjBcEI.top) (979.4 KB)
I believe I have used amber99sb .That’s the thing triggering this error ?
please give your profound insight .
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [May 19, 2023, 7:47pm UTC](https://gromacs.bioexcel.eu/t/error-while-generating-tpr-files/6430/10 "2023-05-19T19:47:51Z")
You cannot mix and match force fields. A force field is a self-consistent entity that relies on systematic balance. A CGenFF topology can only be used with the CHARMM force field. If you’re using AMBER, you need different tools to parametrize ligands, like ACPYPE.
---
### Author:  [@Tanvir](https://gromacs.bioexcel.eu/u/Tanvir)
#### Post date: [May 20, 2023, 5:24pm UTC](https://gromacs.bioexcel.eu/t/error-while-generating-tpr-files/6430/11 "2023-05-20T17:24:22Z")
Thanks a lot. your suggestion solved the error .