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
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
I hope it helps
Alessandra
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.
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.
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 .
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
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
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?
topol.top (979.4 KB)
I believe I have used amber99sb .That’s the thing triggering this error ?
please give your profound insight .
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.
Thanks a lot. your suggestion solved the error .