GROMOS54a7 ff leads to missing parameters in topology after S-S-bonds between Cys residues were app


I tried your inputs (using the same pdb file) using Gromacs version 2023, and I did not encounter any errors (I had to add -maxwarn 1, but that is unrelated.) Did you try this version as well?

I also see a few missing parameters in the .top file, however, I found that gromos54a7.ff/ffbonded.itp contains the following section:

; bond-, angle- and dihedraltypes for specbonds:
[ bondtypes ]
S      S       2    gb_36
NR     FE      2    gb_34

[ angletypes ]
CH1    CH2    S     2   ga_16
CH2    S      S     2   ga_6
CR1    NR    FE     2	ga_34
NR     FE    NR     2   ga_17

[ dihedraltypes ]
S      S      1   gd_21
NR     FE     1   gd_38
CH2    S      1   gd_26

I imagine that those entries are used to fill in the missing parameters around the disulfide bonds.

I recently posted a related question (I did not see your post before): Missing parameters in cyclic peptide with Gromos FF. It might be that this also answers my question, or maybe I can make an FF file with extra parameter entries to fix it…

I hope this helps.