[gmx-users] Applying an improper to S-S bond

[Mark Abraham]

DimitryASuplatov wrote:
> Hello,
> 
> The question is not actually about S-S.
> I have a covalent bond between Cys (SG atom) ang Tyr (CE atom) residues.
> I`ve corrected the specbonds.dat and oplsaa topology to create a new
> residue (tyr2) and I use cys2 topology for cystein.
> 
> During the MD the this covalent bond rotates a lot, so I think of
> applying an improper to the bond. The problem is that the fourth atom of
> a dihedral is always in another residue, I mean that I need the TYR2 CE
> atom to be present in CYS2 topology to set the improper and this is
> obviously impossible.
> 
> 1/ How can I apply improper for this case?

Read and understand the relevant bits of chapters 4 & 5 of the manual, 
and add some suitable function to the .top file by hand.

Mark