[gmx-users] pdb2gmx disulfide bond formation - missing bond, angle, dihedral types with all GROMOS FFs

Hello, I am trying to generate a topology file for my protein which has three disulfide bonds using ffG53a5. I realized in the topology file that the force field parameters for bonds, angle and dihedrals of my S-S bonds are missing. I found the following thread about this issue:

[gmx-users] pdb2gmx disulfide bond formation - missing bond, angle, dihedral types with all GROMOS FFs

Greetings Gromacs Users, I am building the topology file for a protein with three disulfide bonds (bovine pancreatic trpysin inhibitor). When using any of the GROMOS FFs the topol.top output of pdb2gmx has missing bond, angle, and dihedral types on the lines describing the three disulfides.

Re: [gmx-users] pdb2gmx disulfide bond formation - missing bond, angle, dihedral types with all GROMOS FFs

Hi Elizabeth, These missing terms are filled in automatically by grompp from the bondtypes, angletypes and dihedraltypes definitions in the *bon.itp. Unless grompp complains about missing terms, you'll be fine. You can check whether everything is okay by writing out a processed topology (grompp