The bug is present at least in gmx2020.x and 2021.x (bonds and angles are correctly generated) To reproduce it: gmx_mpi pdb2gmx -f 2d4f.pdb -ignh disulfide is between 277 and 878 in this case these are the offending lines (in topol.top [ dihedrals ]) : ``` 273 275 276 277 1 gd_34 273 275 278 280 1 gd_42 273 275 278 280 1 gd_45 109 108 110 124 1 <- wrong 108 110 111 112 1 gd_34 <- wrong 275 278 280 282 1 gd_14 278 280 282 296 1 gd_43 ... 874 876 877 878 1 gd_34 874 876 879 881 1 gd_42 874 876 879 881 1 gd_45 323 326 330 332 1 <- wrong 876 879 881 883 1 gd_14 879 881 883 896 1 gd_43 879 881 883 896 1 gd_44 881 883 884 885 1 gd_34 ``` [2d4f.pdb](/uploads/dc256f25b24868b68a1bb0cb7d7931e5/2d4f.pdb) [topol.top](/uploads/a4bc37f0216677c6394e2fdb2d279156/topol.top)