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1

GROMACS version:2020
GROMACS modification: yes
Here post your question :

i have already writen a topology for jz4(2-propilphenol) and i just want to check it
so i had add ions but i got this error
Fatal error:
Incorrect number of parameters - found 3, expected 6 or 12 for Ryckaert-Bell…
how can i fix this error ?

i really wanted to put my topology right here but im new user and i cant
so i past it here

; Include forcefield parameters
#include “oplsaa.ff/forcefield.itp”

[ moleculetype ]
; Name nrexcl
UNK 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_167 1 UNK OA 1 −0.665 15.99940
2 opls_139 1 UNK CA 1 0.000 12.01100
3 opls_139 1 UNK CB 1 0.000 12.01100
4 opls_145 1 UNK CD 1 -0.115 12.01100
5 opls_145 1 UNK CE 1 -0.115 12.01100
6 opls_145 1 UNK CF 1 -0.115 12.01100
7 opls_139 1 UNK CG 1 0.000 12.01100
8 opls_145 1 UNK CH 1 -0.115 12.01100
9 opls_145 1 UNK CI 1 -0.115 12.01100
10 opls_145 1 UNK CJ 1 -0.115 12.01100
11 opls_140 1 UNK HA 1 0.060 1.00800
12 opls_140 1 UNK HB 1 0.060 1.00800
13 opls_140 1 UNK HC 1 0.060 1.00800
14 opls_140 1 UNK HD 1 0.060 1.00800
15 opls_146 1 UNK HE 1 0.115 1.00800
16 opls_140 1 UNK HF 1 0.060 1.00800
17 opls_140 1 UNK HG 1 0.060 1.00800
18 opls_140 1 UNK HI 1 0.060 1.00800
19 opls_146 1 UNK HJ 1 0.115 1.00800
20 opls_146 1 UNK HK 1 0.115 1.00800
21 opls_146 1 UNK HL 1 0.115 1.00800
22 opls_168 1 UNK HM 1 0.475 1.00800

[ bonds ]
; ai aj fu
10 21 1
10 8 1
10 9 1
8 19 1
8 5 1
9 20 1
9 6 1
6 15 1
6 4 1
5 4 1
5 1 1
1 22 1
4 2 1
2 12 1
2 11 1
2 3 1
3 13 1
3 14 1
3 7 1
7 16 1
7 17 1
7 18 1

[ pairs ]
; ai aj fu
21 19 1
21 5 1
21 20 1
21 6 1
10 1 1
10 4 1
10 15 1
19 1 1
19 4 1
19 9 1
8 22 1
8 6 1
8 20 1
8 2 1
20 15 1
20 4 1
9 5 1
9 2 1
15 5 1
15 2 1
6 1 1
6 12 1
6 11 1
6 3 1
5 11 1
5 12 1
5 3 1
1 2 1
22 4 1
4 13 1
4 14 1
4 7 1
2 17 1
2 18 1
2 16 1
12 13 1
12 14 1
12 7 1
11 13 1
11 14 1
11 7 1
13 17 1
13 18 1
13 16 1
14 16 1
14 17 1
14 18 1

[ angles ]
; ai aj ak funct
8 10 21 1
21 10 9 1
8 10 9 1
19 8 10 1
19 8 5 1
5 8 10 1
1 5 8 1
8 5 4 1
1 5 4 1
22 1 5 1
10 9 20 1
10 9 6 1
6 9 20 1
4 6 15 1
4 6 9 1
15 6 9 1
5 4 6 1
2 4 6 1
5 4 2 1
12 2 4 1
12 2 3 1
12 2 11 1
4 2 11 1
3 2 11 1
4 2 3 1
3 7 16 1
2 3 7 1
13 3 14 1
13 3 2 1
13 3 7 1
7 3 14 1
2 3 14 1
17 7 6 1
3 7 18 1
3 7 17 1
17 7 18 1
18 7 16 1

[ dihedrals ]
; PROPER DIHEDRAL ANGLES
; ai aj ak al funct
19 8 10 21 3
19 8 10 9 3
19 8 5 1 3
19 8 5 4 3
8 5 1 22 3
8 5 4 6 3
8 5 4 2 3
8 10 9 20 3
8 10 9 6 3
21 10 8 5 3
21 10 9 20 3
21 10 9 6 3
10 9 6 15 3
10 9 6 14 3
10 8 5 1 3
10 8 5 4 3
20 9 6 15 3
20 9 6 4 3
9 6 4 5 3
9 6 4 2 3
9 10 8 5 3
15 6 4 5 3
15 6 4 2 3
6 4 5 1 3
6 4 2 12 3
6 4 2 11 3
6 4 2 3 3
5 4 2 12 3
5 4 2 11 3
5 4 2 3 3
1 5 4 2 3
22 1 5 4 3
4 2 3 7 3
4 2 3 13 3
4 2 3 14 3
2 3 7 17 3
2 3 7 18 3
2 3 7 16 3
12 2 3 13 3
12 2 3 14 3
12 2 3 7 3
11 2 3 13 3
11 2 3 14 3
11 2 3 7 3
13 3 7 16 3
13 3 7 17 3
13 3 7 18 3
14 3 7 16 3
14 3 7 17 3
14 3 7 18 3

[ dihedrals ]
; IMPROPER DIHEDRAL ANGLES
; ai aj ak al funct
9 6 4 15 3 improper_Z_CA_X_Y
10 8 5 19 3 improper_Z_CA_X_Y
2 4 5 6 3 improper_Z_CA_X_Y
20 9 10 6 3 improper_Z_CA_X_Y
21 10 8 9 3 improper_Z_CA_X_Y
1 5 4 8 3 improper_Z_CA_X_Y

thanks for your help

2

Hi,

Do you use the standard opls force field? Or a modified version?

/Alessandra

3

Hi again,

The error says that only 3 parameters are provided to define the dihedral potential while the function (nr 3) corresponds to Ryckaert-Bellemans dihedral (that want 6 parameters) (see table below).

https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html?highlight=force%20field%20table

My guess is that some dihedral (parameter or function) are not properly/consistently defined among topology file and the force field files

I hope it helps
\Alessandra

4

Hi
I’m really thankful for your help
Bests

Kimia shahbazi
Sharif university of technology