[gmx-users] SS bond forcing

[Pierre THEVENET]

Ok. Thank you for your help. I will try to do it and see if it not too time
consuming.

--------------------------

Pierre THEVENET
Ph.D. Candidate
INSERM - MTi
Ecole Doctorale B3MI
Université Paris Diderot - Paris 7




2012/4/10 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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