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

DimitryASuplatov genesup at gmail.com
Wed Mar 25 18:24:38 CET 2009


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?
2/ Any other (simpler) ways to freez the rotation?


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