Duplicates of rows of angles and dihedrals for groups containing Cl

User discussions
1

GROMACS version: 2026.1
GROMACS modification: Yes (I added my own RTP file for a modified cysteine residue that includes the fluorescent label AF546)
Hello everyone!

I have created an RTP file for the fluorescent dye AF546. I used the GAFF2 force field to describe the atom types. I added the created RTP file to the amber14sb force field directory.

AF_546_cys_rtp.txt (36.1 KB)

imgsrv
imgsrv300×300 2.68 KB

When running pdb2gmx, the topol.top file was generated successfully. However, during subsequent system preparation for MD simulation, at the stage of adding Na/Cl ions, I encountered the following error:
ERROR 1 [file topol.top, line 832]:
No default Angle types for interaction
‘60 61 64 1’.

ERROR 2 [file topol.top, line 835]:
No default Angle types for interaction
‘63 61 64 1’.

ERROR 3 [file topol.top, line 837]:
No default Angle types for interaction
‘60 62 65 1’.

ERROR 4 [file topol.top, line 839]:
No default Angle types for interaction
‘65 62 66 1’.

ERROR 5 [file topol.top, line 846]:
No default Angle types for interaction
‘62 66 69 1’.

ERROR 6 [file topol.top, line 847]:
No default Angle types for interaction
‘67 66 69 1’.

ERROR 7 [file topol.top, line 1187]:
No default Proper Dih. types for interaction
‘59 60 61 64 9’.

ERROR 8 [file topol.top, line 1189]:
No default Proper Dih. types for interaction
‘62 60 61 64 9’.

ERROR 9 [file topol.top, line 1193]:
No default Proper Dih. types for interaction
‘59 60 62 65 9’.

ERROR 10 [file topol.top, line 1195]:
No default Proper Dih. types for interaction
‘61 60 62 65 9’.

ERROR 11 [file topol.top, line 1199]:
No default Proper Dih. types for interaction
‘64 61 63 67 9’.

ERROR 12 [file topol.top, line 1201]:
No default Proper Dih. types for interaction
‘64 61 63 68 9’.

ERROR 13 [file topol.top, line 1204]:
No default Proper Dih. types for interaction
‘60 62 66 69 9’.

ERROR 14 [file topol.top, line 1206]:
No default Proper Dih. types for interaction
‘65 62 66 67 9’.

ERROR 15 [file topol.top, line 1208]:
No default Proper Dih. types for interaction
‘65 62 66 69 9’.

ERROR 16 [file topol.top, line 1220]:
No default Proper Dih. types for interaction
‘69 66 67 63 9’.

ERROR 17 [file topol.top, line 1221]:
No default Proper Dih. types for interaction
‘69 66 67 70 9’.

As a result, when using pdb2gmx, duplicate lines are generated in my topol.top file. Below is a fragment of my topol.top file:

topol.top (58.7 KB)

60 61 64 1
60 61 64 1 119.3800 536.0
63 61 64 1 119.3800 536.0
63 61 64 1
60 62 65 1 119.3800 536.0
60 62 65 1
60 62 66 1 120.0200 532.8
65 62 66 1
65 62 66 1 119.3800 536.0

The same issue occurs in the [ dihedrals ] section, but there the duplicates also include equivalent reverse entries (e.g., a b c d is considered equivalent to d c b a).
69 66 67 63 9
69 66 67 70 9
69 66 67 70 9 180.000 15.1670 2
63 67 66 69 9 180.000 15.1670 2

What is the cause of duplicate lines in angles and dihedrals? Is the best solution simply to remove the duplicate lines manually?

2

Probably the MOL2 file was not properly parameterized, and not all interactions — especially angle and dihedral parameters — were generated correctly. If you are using tleap, you usually also need an frcmod file to provide the missing parameters.