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

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 25 18:33:52 CET 2009

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

Probably a dihedral restraint is more appropriate.


> Thanks
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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