[gmx-users] disulfide bridges

[Miro Astore]

Oh thank you so much, I did not know it was a reference value. Given a
range of values might exist in one system I'm guessing minimization would
be the only way to deal with such a situation.

Best, Miro

On Sat, May 2, 2020 at 9:53 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/2/20 6:54 AM, Miro Astore wrote:
> > Hi all,
> >
> > I'm trying to make a protein with a fair few disulfide bridges and I
> > couldn't get it to work. I chose -ss yes and increased the minimum
> distance
> > in specbonds.dat but it doesn't seem to want to let me see all possible
> > pariings.
>
> specbond.dat does not set minimum distances. It sets a reference value,
> and a bond is only assigned if the distance in the coordinate file is
> within 10% of that reference. So if you were, for example, to increase
> the value from 0.2 nm (conventional) to 0.3 nm, you'll miss the
> disulfides that should be formed because the new reference range is 0.27
> - 0.33 nm and anything between 0.18 - 0.22 nm will not be assigned a
> disulfide linkage.
>
> > Any way I can nudge it in the right direction without performing a
> > minimisation with restraints?
>
> Depends on the range of distances in your structure, but this is often
> what you have to do.
>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
> Assistant Professor
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-- 
Miro A. Astore   (he/him)
PhD Candidate | Computational Biophysics
Office 434 A28 School of Physics
University of Sydney