[gmx-users] SS bond forcing

[Justin A. Lemkul]

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.

http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints

> 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:

http://www.gromacs.org/Documentation/How-tos/Distance_Restraints

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

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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