[gmx-users] SS bond forcing

[Justin A. Lemkul]

Pierre THEVENET wrote:
> In most cases (it is form predicted structures) if the bonds is not 
> formes, the S atoms are at the opposite side of the backbone. And I work 
> on peptides, so the length of the structure isn't that big (50 residues max)
> 

Well, if you try the distance restraint approach, I'd do it in the absence of 
any solvent since there likely will be rather large structural changes (and thus 
very fast protein-solvent clashes as the restraints are satisfied), unless the 
peptide is pretty compact.  Really short MD should tell you if this will even be 
feasible.

-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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