How to solve the “No default Proper Dih. types?”

User discussions
1

GROMACS version:2021.1
GROMACS modification: No
Hello Justin,
I am carrying out MD study for a system consist of a protein and polyol using charmm36-feb2021.ff and for parametrization i used CGenFF server version 4.6 previously and did all the simulations properly. But now i need to do one more polyol parameters to complete my study. Due to the up-gradation of CGenFF server to version-4.6 it might be using latest charmm force field and the itp file i am getting from the str file is showing error in the grompp step for energy minimization.
ERROR 1[file 123bto.itp, line 131]:
No default proper Dih. types

there is only 1 error corresponds to proper dihedrals.

if i remove the line from the itp file i am able to do energy minimization.

I am not sure is it fine for my study or it will generate different result . Please guide me to sort out this error.
I am attaching the itp file for the polyol molecule (in dihedral 14th row) for your reference
; Created by cgenff_charmm2gmx_py3_nx1.py

[ moleculetype ]
; Name nrexcl
123BTO 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 20497 rtp 20497 q qsum
1 OG311 1 20497 O1 1 -0.650 15.999 ;
2 OG311 1 20497 O2 2 -0.643 15.999 ;
3 OG311 1 20497 O3 3 -0.646 15.999 ;
4 CG311 1 20497 C1 4 0.147 12.011 ;
5 CG311 1 20497 C2 5 0.120 12.011 ;
6 CG321 1 20497 C3 6 0.056 12.011 ;
7 CG331 1 20497 C4 7 -0.267 12.011 ;
8 HGA1 1 20497 H1 8 0.090 1.008 ;
9 HGA1 1 20497 H2 9 0.090 1.008 ;
10 HGA2 1 20497 H3 10 0.090 1.008 ;
11 HGA2 1 20497 H4 11 0.090 1.008 ;
12 HGA3 1 20497 H5 12 0.090 1.008 ;
13 HGA3 1 20497 H6 13 0.090 1.008 ;
14 HGA3 1 20497 H7 14 0.090 1.008 ;
15 HGP1 1 20497 H8 15 0.420 1.008 ;
16 HGP1 1 20497 H9 16 0.414 1.008 ;
17 HGP1 1 20497 H10 17 0.419 1.008 ;

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 4 1
1 15 1
2 5 1
2 16 1
3 6 1
3 17 1
4 5 1
4 6 1
4 8 1
5 7 1
5 9 1
6 10 1
6 11 1
7 12 1
7 13 1
7 14 1

[ pairs ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 7 1
1 9 1
1 3 1
1 10 1
1 11 1
2 6 1
2 8 1
2 12 1
2 13 1
2 14 1
3 5 1
3 8 1
4 16 1
4 17 1
4 12 1
4 13 1
4 14 1
5 15 1
5 10 1
5 11 1
6 15 1
6 7 1
6 9 1
7 16 1
7 8 1
8 15 1
8 9 1
8 10 1
8 11 1
9 16 1
9 12 1
9 13 1
9 14 1
10 17 1
11 17 1

[ angles ]
; ai aj ak funct c0 c1 c2 c3
4 1 15 5
5 2 16 5
6 3 17 5
1 4 5 5
1 4 6 5
1 4 8 5
5 4 6 5
5 4 8 5
6 4 8 5
2 5 4 5
2 5 7 5
2 5 9 5
4 5 7 5
4 5 9 5
7 5 9 5
3 6 4 5
3 6 10 5
3 6 11 5
4 6 10 5
4 6 11 5
10 6 11 5
5 7 12 5
5 7 13 5
5 7 14 5
12 7 13 5
12 7 14 5
13 7 14 5

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
15 1 4 5 9
15 1 4 6 9
15 1 4 8 9
16 2 5 4 9
16 2 5 7 9
16 2 5 9 9
17 3 6 4 9
17 3 6 10 9
17 3 6 11 9
1 4 5 2 9
1 4 5 7 9
1 4 5 9 9
6 4 5 2 9
6 4 5 7 9
6 4 5 9 9
8 4 5 2 9
8 4 5 7 9
8 4 5 9 9
1 4 6 3 9
1 4 6 10 9
1 4 6 11 9
5 4 6 3 9
5 4 6 10 9
5 4 6 11 9
8 4 6 3 9
8 4 6 10 9
8 4 6 11 9
2 5 7 12 9
2 5 7 13 9
2 5 7 14 9
4 5 7 12 9
4 5 7 13 9
4 5 7 14 9
9 5 7 12 9
9 5 7 13 9
9 5 7 14 9

  1. List item

Your help is much appreciated.

Thanks;

2

You can’t simply delete dihedrals that generate errors. You need to solve the actual problem.

I can’t make any suggestion without knowing what sequence of atom types is generating the problem, but if you generated the topology with CGenFF version 4.6 and are using the latest C36 port, this shouldn’t happen. But I would have to cross-reference the original CHARMM force field files to know for sure. Make sure that if the .str → .itp conversion process generates a .prm file, you are appropriately adding an #include statement for it to call the newly generated parameters.

3

Thank you for your valuable suggestions. Actually in charmm36-feb2021
CG321 CG311 CG311 CG331 9 180.0000000 2.092000 4
dihedral was missing and I took it from charmm36-july2022 and after adding it to ffbonded.itp under [dihedral.types] in charmm36-feb2021 the problem got resolved.

Kind regards,
Subhasree