[gmx-users] SS bond forcing

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 10 16:17:52 CEST 2012

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 



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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