[gmx-users] SS bond forcing

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 6 17:19:03 CEST 2012

pithevenet at free.fr wrote:
> Dear gmx users,
> I try to use gmx to make some minimization. Unfortunatly, I have some SS
> bonds which are not formed in my PDB because the S-S atoms are too far away
> to connect to each other. I saw at that page :
> http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds that it
> is possible to force GROMACS to make bonds with sulfur atoms by adding a
> distant constrains between the atoms.

Note that constraints and restraints are different.


> But I didn't understand in which file it should be inserted and at which
> step. Can you help me?

If you want to restrain S-S distances to force a more amenable geometry for 
disulfide formation, what you need are distance restraints in the .top:


Refer to the manual section and figures cited on that page for more information.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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