GROMACS version: 2018.4
GROMACS modification: No
pdb2gmx does not check if the involved residues were already connected by a ss bond during the automatic usage of specbond.dat. (multiple peptide chains in a pdb file separated with “TER” should be crosslinked via disulfide bridges).
This leads to a topology file which contains angles like SG-SG-SG and dihedrals of CB-SG-SG-SG (SG is the sulfur atom in the CYS residue). There are obviously no parameters for these type of angles, so grompp throws error messages of missing interaction types.
Is there any solution to this? Did I miss somewhere an option making sure pdb2gmx only ever connects two sulfur atoms with each other?